SMTL ID : 4mu4.1

The form B structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and its substrate, 2R3S-IGP, to 1.41 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-24-mer

Ligands

48 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.72 Chain W: H.45, H.167, E.171 Ligands: IYP.3 4 PLIP interactions: 3 interactions with chain W, 1 interactions with chain A Metal complexes: W:H.45, W:H.167, W:E.171, A:H.72 MN.2: 5 residues within 4Å: Chain A: H.71, E.75, H.143 Chain W: H.168 Ligands: IYP.3 5 PLIP interactions: 1 interactions with chain W, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: W:H.168, A:H.71, A:E.75, A:H.143, H2O.1 MN.7: 5 residues within 4Å: Chain B: H.72 Chain V: H.45, H.167, E.171 Ligands: IYP.9 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain B Metal complexes: V:H.45, V:H.167, V:E.171, B:H.72 MN.8: 5 residues within 4Å: Chain B: H.71, E.75, H.143 Chain V: H.168 Ligands: IYP.9 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain V, 1 Ligand-Water interactions Metal complexes: B:H.71, B:E.75, B:H.143, V:H.168, H2O.8 MN.13: 5 residues within 4Å: Chain C: H.72 Chain U: H.45, H.167, E.171 Ligands: IYP.15 4 PLIP interactions: 3 interactions with chain U, 1 interactions with chain C Metal complexes: U:H.45, U:H.167, U:E.171, C:H.72 MN.14: 5 residues within 4Å: Chain C: H.71, E.75, H.143 Chain U: H.168 Ligands: IYP.15 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain U, 1 Ligand-Water interactions Metal complexes: C:H.71, C:E.75, C:H.143, U:H.168, H2O.16 MN.19: 5 residues within 4Å: Chain D: H.72 Chain X: H.45, H.167, E.171 Ligands: IYP.21 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain D Metal complexes: X:H.45, X:H.167, X:E.171, D:H.72 MN.20: 5 residues within 4Å: Chain D: H.71, E.75, H.143 Chain X: H.168 Ligands: IYP.21 5 PLIP interactions: 1 interactions with chain X, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: X:H.168, D:H.71, D:E.75, D:H.143, H2O.23 MN.25: 5 residues within 4Å: Chain E: H.72 Chain T: H.45, H.167, E.171 Ligands: IYP.27 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain E Metal complexes: T:H.45, T:H.167, T:E.171, E:H.72 MN.26: 5 residues within 4Å: Chain E: H.71, E.75, H.143 Chain T: H.168 Ligands: IYP.27 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain T, 1 Ligand-Water interactions Metal complexes: E:H.71, E:E.75, E:H.143, T:H.168, H2O.31 MN.31: 5 residues within 4Å: Chain F: H.72 Chain Q: H.45, H.167, E.171 Ligands: IYP.33 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain F Metal complexes: Q:H.45, Q:H.167, Q:E.171, F:H.72 MN.32: 5 residues within 4Å: Chain F: H.71, E.75, H.143 Chain Q: H.168 Ligands: IYP.33 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: F:H.71, F:E.75, F:H.143, Q:H.168, H2O.38 MN.37: 5 residues within 4Å: Chain G: H.72 Chain R: H.45, H.167, E.171 Ligands: IYP.39 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain G Metal complexes: R:H.45, R:H.167, R:E.171, G:H.72 MN.38: 5 residues within 4Å: Chain G: H.71, E.75, H.143 Chain R: H.168 Ligands: IYP.39 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: G:H.71, G:E.75, G:H.143, R:H.168, H2O.46 MN.43: 5 residues within 4Å: Chain H: H.72 Chain S: H.45, H.167, E.171 Ligands: IYP.45 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain S Metal complexes: H:H.72, S:H.45, S:H.167, S:E.171 MN.44: 5 residues within 4Å: Chain H: H.71, E.75, H.143 Chain S: H.168 Ligands: IYP.45 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain S, 1 Ligand-Water interactions Metal complexes: H:H.71, H:E.75, H:H.143, S:H.168, H2O.53 MN.49: 5 residues within 4Å: Chain I: H.72 Chain M: H.45, H.167, E.171 Ligands: IYP.51 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain I Metal complexes: M:H.45, M:H.167, M:E.171, I:H.72 MN.50: 5 residues within 4Å: Chain I: H.71, E.75, H.143 Chain M: H.168 Ligands: IYP.51 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: I:H.71, I:E.75, I:H.143, M:H.168, H2O.61 MN.55: 5 residues within 4Å: Chain J: H.72 Chain P: H.45, H.167, E.171 Ligands: IYP.57 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain J Metal complexes: P:H.45, P:H.167, P:E.171, J:H.72 MN.56: 5 residues within 4Å: Chain J: H.71, E.75, H.143 Chain P: H.168 Ligands: IYP.57 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: J:H.71, J:E.75, J:H.143, P:H.168, H2O.68 MN.61: 5 residues within 4Å: Chain K: H.72 Chain O: H.45, H.167, E.171 Ligands: IYP.63 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain K Metal complexes: O:H.45, O:H.167, O:E.171, K:H.72 MN.62: 5 residues within 4Å: Chain K: H.71, E.75, H.143 Chain O: H.168 Ligands: IYP.63 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: K:H.71, K:E.75, K:H.143, O:H.168, H2O.76 MN.67: 5 residues within 4Å: Chain L: H.72 Chain N: H.45, H.167, E.171 Ligands: IYP.69 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain L Metal complexes: N:H.45, N:H.167, N:E.171, L:H.72 MN.68: 5 residues within 4Å: Chain L: H.71, E.75, H.143 Chain N: H.168 Ligands: IYP.69 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: L:H.71, L:E.75, L:H.143, N:H.168, H2O.83 MN.73: 5 residues within 4Å: Chain K: H.45, H.167, E.171 Chain M: H.72 Ligands: IYP.75 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain M Metal complexes: K:H.45, K:H.167, K:E.171, M:H.72 MN.74: 5 residues within 4Å: Chain K: H.168 Chain M: H.71, E.75, H.143 Ligands: IYP.75 5 PLIP interactions: 3 interactions with chain M, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: M:H.71, M:E.75, M:H.143, K:H.168, H2O.91 MN.79: 5 residues within 4Å: Chain J: H.45, H.167, E.171 Chain N: H.72 Ligands: IYP.81 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain N Metal complexes: J:H.45, J:H.167, J:E.171, N:H.72 MN.80: 5 residues within 4Å: Chain J: H.168 Chain N: H.71, E.75, H.143 Ligands: IYP.81 5 PLIP interactions: 3 interactions with chain N, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: N:H.71, N:E.75, N:H.143, J:H.168, H2O.99 MN.85: 5 residues within 4Å: Chain I: H.45, H.167, E.171 Chain O: H.72 Ligands: IYP.87 4 PLIP interactions: 1 interactions with chain O, 3 interactions with chain I Metal complexes: O:H.72, I:H.45, I:H.167, I:E.171 MN.86: 5 residues within 4Å: Chain I: H.168 Chain O: H.71, E.75, H.143 Ligands: IYP.87 5 PLIP interactions: 3 interactions with chain O, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: O:H.71, O:E.75, O:H.143, I:H.168, H2O.106 MN.91: 5 residues within 4Å: Chain L: H.45, H.167, E.171 Chain P: H.72 Ligands: IYP.93 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain P Metal complexes: L:H.45, L:H.167, L:E.171, P:H.72 MN.92: 5 residues within 4Å: Chain L: H.168 Chain P: H.71, E.75, H.143 Ligands: IYP.93 5 PLIP interactions: 3 interactions with chain P, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: P:H.71, P:E.75, P:H.143, L:H.168, H2O.114 MN.97: 5 residues within 4Å: Chain H: H.45, H.167, E.171 Chain Q: H.72 Ligands: IYP.99 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain Q Metal complexes: H:H.45, H:H.167, H:E.171, Q:H.72 MN.98: 5 residues within 4Å: Chain H: H.168 Chain Q: H.71, E.75, H.143 Ligands: IYP.99 5 PLIP interactions: 1 interactions with chain H, 3 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: H:H.168, Q:H.71, Q:E.75, Q:H.143, H2O.121 MN.103: 5 residues within 4Å: Chain E: H.45, H.167, E.171 Chain R: H.72 Ligands: IYP.105 4 PLIP interactions: 1 interactions with chain R, 3 interactions with chain E Metal complexes: R:H.72, E:H.45, E:H.167, E:E.171 MN.104: 5 residues within 4Å: Chain E: H.168 Chain R: H.71, E.75, H.143 Ligands: IYP.105 5 PLIP interactions: 3 interactions with chain R, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: R:H.71, R:E.75, R:H.143, E:H.168, H2O.129 MN.109: 5 residues within 4Å: Chain F: H.45, H.167, E.171 Chain S: H.72 Ligands: IYP.111 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain S Metal complexes: F:H.45, F:H.167, F:E.171, S:H.72 MN.110: 5 residues within 4Å: Chain F: H.168 Chain S: H.71, E.75, H.143 Ligands: IYP.111 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain S, 1 Ligand-Water interactions Metal complexes: F:H.168, S:H.71, S:E.75, S:H.143, H2O.136 MN.115: 5 residues within 4Å: Chain G: H.45, H.167, E.171 Chain T: H.72 Ligands: IYP.117 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain T Metal complexes: G:H.45, G:H.167, G:E.171, T:H.72 MN.116: 5 residues within 4Å: Chain G: H.168 Chain T: H.71, E.75, H.143 Ligands: IYP.117 5 PLIP interactions: 3 interactions with chain T, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: T:H.71, T:E.75, T:H.143, G:H.168, H2O.144 MN.121: 5 residues within 4Å: Chain A: H.45, H.167, E.171 Chain U: H.72 Ligands: IYP.123 4 PLIP interactions: 1 interactions with chain U, 3 interactions with chain A Metal complexes: U:H.72, A:H.45, A:H.167, A:E.171 MN.122: 5 residues within 4Å: Chain A: H.168 Chain U: H.71, E.75, H.143 Ligands: IYP.123 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: A:H.168, U:H.71, U:E.75, U:H.143, H2O.151 MN.127: 5 residues within 4Å: Chain D: H.45, H.167, E.171 Chain V: H.72 Ligands: IYP.129 4 PLIP interactions: 1 interactions with chain V, 3 interactions with chain D Metal complexes: V:H.72, D:H.45, D:H.167, D:E.171 MN.128: 5 residues within 4Å: Chain D: H.168 Chain V: H.71, E.75, H.143 Ligands: IYP.129 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: D:H.168, V:H.71, V:E.75, V:H.143, H2O.159 MN.133: 5 residues within 4Å: Chain C: H.45, H.167, E.171 Chain W: H.72 Ligands: IYP.135 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain W Metal complexes: C:H.45, C:H.167, C:E.171, W:H.72 MN.134: 5 residues within 4Å: Chain C: H.168 Chain W: H.71, E.75, H.143 Ligands: IYP.135 5 PLIP interactions: 3 interactions with chain W, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: W:H.71, W:E.75, W:H.143, C:H.168, H2O.166 MN.139: 5 residues within 4Å: Chain B: H.45, H.167, E.171 Chain X: H.72 Ligands: IYP.141 4 PLIP interactions: 1 interactions with chain X, 3 interactions with chain B Metal complexes: X:H.72, B:H.45, B:H.167, B:E.171 MN.140: 5 residues within 4Å: Chain B: H.168 Chain X: H.71, E.75, H.143 Ligands: IYP.141 5 PLIP interactions: 3 interactions with chain X, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: X:H.71, X:E.75, X:H.143, B:H.168, H2O.174

24 x IYP: (2R,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate(Non-covalent)

IYP.3: 15 residues within 4Å: Chain A: H.71, H.72, E.75 Chain M: R.97, R.119, S.197, S.198, K.199 Chain W: H.45, H.167, H.168, E.171, K.175 Ligands: MN.1, MN.2 8 PLIP interactions: 7 interactions with chain M, 1 interactions with chain W Hydrogen bonds: M:R.119, M:S.198 Water bridges: M:R.97, M:R.97 Salt bridges: M:R.97, M:R.119, M:K.199, W:K.175 IYP.9: 15 residues within 4Å: Chain B: H.71, H.72, E.75 Chain N: R.97, R.119, S.197, S.198, K.199 Chain V: H.45, H.167, H.168, E.171, K.175 Ligands: MN.7, MN.8 8 PLIP interactions: 7 interactions with chain N, 1 interactions with chain V Hydrogen bonds: N:R.119, N:S.198 Water bridges: N:R.97, N:R.97 Salt bridges: N:R.97, N:R.119, N:K.199, V:K.175 IYP.15: 15 residues within 4Å: Chain C: H.71, H.72, E.75 Chain P: R.97, R.119, S.197, S.198, K.199 Chain U: H.45, H.167, H.168, E.171, K.175 Ligands: MN.13, MN.14 8 PLIP interactions: 7 interactions with chain P, 1 interactions with chain U Hydrogen bonds: P:R.119, P:S.198 Water bridges: P:R.97, P:R.119 Salt bridges: P:R.97, P:R.119, P:K.199, U:K.175 IYP.21: 15 residues within 4Å: Chain D: H.71, H.72, E.75 Chain O: R.97, R.119, S.197, S.198, K.199 Chain X: H.45, H.167, H.168, E.171, K.175 Ligands: MN.19, MN.20 8 PLIP interactions: 1 interactions with chain X, 7 interactions with chain O Salt bridges: X:K.175, O:R.97, O:R.119, O:K.199 Hydrogen bonds: O:R.119, O:S.198 Water bridges: O:R.97, O:R.119 IYP.27: 15 residues within 4Å: Chain E: H.71, H.72, E.75 Chain T: H.45, H.167, H.168, E.171, K.175 Chain W: R.97, R.119, S.197, S.198, K.199 Ligands: MN.25, MN.26 8 PLIP interactions: 7 interactions with chain W, 1 interactions with chain T Hydrogen bonds: W:R.119, W:S.198 Water bridges: W:R.97, W:R.119 Salt bridges: W:R.97, W:R.119, W:K.199, T:K.175 IYP.33: 15 residues within 4Å: Chain F: H.71, H.72, E.75 Chain Q: H.45, H.167, H.168, E.171, K.175 Chain X: R.97, R.119, S.197, S.198, K.199 Ligands: MN.31, MN.32 8 PLIP interactions: 7 interactions with chain X, 1 interactions with chain Q Hydrogen bonds: X:R.119, X:S.198 Water bridges: X:R.97, X:R.97 Salt bridges: X:R.97, X:R.119, X:K.199, Q:K.175 IYP.39: 15 residues within 4Å: Chain G: H.71, H.72, E.75 Chain R: H.45, H.167, H.168, E.171, K.175 Chain V: R.97, R.119, S.197, S.198, K.199 Ligands: MN.37, MN.38 8 PLIP interactions: 7 interactions with chain V, 1 interactions with chain R Hydrogen bonds: V:R.119, V:S.198 Water bridges: V:R.97, V:R.119 Salt bridges: V:R.97, V:R.119, V:K.199, R:K.175 IYP.45: 15 residues within 4Å: Chain H: H.71, H.72, E.75 Chain S: H.45, H.167, H.168, E.171, K.175 Chain U: R.97, R.119, S.197, S.198, K.199 Ligands: MN.43, MN.44 8 PLIP interactions: 7 interactions with chain U, 1 interactions with chain S Hydrogen bonds: U:R.119, U:S.198 Water bridges: U:R.97, U:R.97 Salt bridges: U:R.97, U:R.119, U:K.199, S:K.175 IYP.51: 15 residues within 4Å: Chain I: H.71, H.72, E.75 Chain M: H.45, H.167, H.168, E.171, K.175 Chain T: R.97, R.119, S.197, S.198, K.199 Ligands: MN.49, MN.50 8 PLIP interactions: 7 interactions with chain T, 1 interactions with chain M Hydrogen bonds: T:R.119, T:S.198 Water bridges: T:R.97, T:R.97 Salt bridges: T:R.97, T:R.119, T:K.199, M:K.175 IYP.57: 15 residues within 4Å: Chain J: H.71, H.72, E.75 Chain P: H.45, H.167, H.168, E.171, K.175 Chain S: R.97, R.119, S.197, S.198, K.199 Ligands: MN.55, MN.56 8 PLIP interactions: 7 interactions with chain S, 1 interactions with chain P Hydrogen bonds: S:R.119, S:S.198 Water bridges: S:R.97, S:R.119 Salt bridges: S:R.97, S:R.119, S:K.199, P:K.175 IYP.63: 15 residues within 4Å: Chain K: H.71, H.72, E.75 Chain O: H.45, H.167, H.168, E.171, K.175 Chain Q: R.97, R.119, S.197, S.198, K.199 Ligands: MN.61, MN.62 8 PLIP interactions: 1 interactions with chain O, 7 interactions with chain Q Salt bridges: O:K.175, Q:R.97, Q:R.119, Q:K.199 Hydrogen bonds: Q:R.119, Q:S.198 Water bridges: Q:R.97, Q:R.119 IYP.69: 15 residues within 4Å: Chain L: H.71, H.72, E.75 Chain N: H.45, H.167, H.168, E.171, K.175 Chain R: R.97, R.119, S.197, S.198, K.199 Ligands: MN.67, MN.68 8 PLIP interactions: 7 interactions with chain R, 1 interactions with chain N Hydrogen bonds: R:R.119, R:S.198 Water bridges: R:R.97, R:R.97 Salt bridges: R:R.97, R:R.119, R:K.199, N:K.175 IYP.75: 15 residues within 4Å: Chain A: R.97, R.119, S.197, S.198, K.199 Chain K: H.45, H.167, H.168, E.171, K.175 Chain M: H.71, H.72, E.75 Ligands: MN.73, MN.74 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain K Hydrogen bonds: A:R.119, A:S.198 Water bridges: A:R.97, A:R.119 Salt bridges: A:R.97, A:R.119, A:K.199, K:K.175 IYP.81: 15 residues within 4Å: Chain B: R.97, R.119, S.197, S.198, K.199 Chain J: H.45, H.167, H.168, E.171, K.175 Chain N: H.71, H.72, E.75 Ligands: MN.79, MN.80 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain J Hydrogen bonds: B:R.119, B:S.198 Water bridges: B:R.97, B:R.119 Salt bridges: B:R.97, B:R.119, B:K.199, J:K.175 IYP.87: 15 residues within 4Å: Chain D: R.97, R.119, S.197, S.198, K.199 Chain I: H.45, H.167, H.168, E.171, K.175 Chain O: H.71, H.72, E.75 Ligands: MN.85, MN.86 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain I Hydrogen bonds: D:R.119, D:S.198 Water bridges: D:R.97, D:R.97 Salt bridges: D:R.97, D:R.119, D:K.199, I:K.175 IYP.93: 15 residues within 4Å: Chain C: R.97, R.119, S.197, S.198, K.199 Chain L: H.45, H.167, H.168, E.171, K.175 Chain P: H.71, H.72, E.75 Ligands: MN.91, MN.92 8 PLIP interactions: 1 interactions with chain L, 7 interactions with chain C Salt bridges: L:K.175, C:R.97, C:R.119, C:K.199 Hydrogen bonds: C:R.119, C:S.198 Water bridges: C:R.97, C:R.97 IYP.99: 15 residues within 4Å: Chain H: H.45, H.167, H.168, E.171, K.175 Chain K: R.97, R.119, S.197, S.198, K.199 Chain Q: H.71, H.72, E.75 Ligands: MN.97, MN.98 8 PLIP interactions: 1 interactions with chain H, 7 interactions with chain K Salt bridges: H:K.175, K:R.97, K:R.119, K:K.199 Hydrogen bonds: K:R.119, K:S.198 Water bridges: K:R.97, K:R.97 IYP.105: 15 residues within 4Å: Chain E: H.45, H.167, H.168, E.171, K.175 Chain L: R.97, R.119, S.197, S.198, K.199 Chain R: H.71, H.72, E.75 Ligands: MN.103, MN.104 8 PLIP interactions: 1 interactions with chain E, 7 interactions with chain L Salt bridges: E:K.175, L:R.97, L:R.119, L:K.199 Hydrogen bonds: L:R.119, L:S.198 Water bridges: L:R.97, L:R.119 IYP.111: 15 residues within 4Å: Chain F: H.45, H.167, H.168, E.171, K.175 Chain J: R.97, R.119, S.197, S.198, K.199 Chain S: H.71, H.72, E.75 Ligands: MN.109, MN.110 8 PLIP interactions: 7 interactions with chain J, 1 interactions with chain F Hydrogen bonds: J:R.119, J:S.198 Water bridges: J:R.97, J:R.97 Salt bridges: J:R.97, J:R.119, J:K.199, F:K.175 IYP.117: 15 residues within 4Å: Chain G: H.45, H.167, H.168, E.171, K.175 Chain I: R.97, R.119, S.197, S.198, K.199 Chain T: H.71, H.72, E.75 Ligands: MN.115, MN.116 8 PLIP interactions: 1 interactions with chain G, 7 interactions with chain I Salt bridges: G:K.175, I:R.97, I:R.119, I:K.199 Hydrogen bonds: I:R.119, I:S.198 Water bridges: I:R.97, I:R.119 IYP.123: 15 residues within 4Å: Chain A: H.45, H.167, H.168, E.171, K.175 Chain H: R.97, R.119, S.197, S.198, K.199 Chain U: H.71, H.72, E.75 Ligands: MN.121, MN.122 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:R.119, H:S.198 Water bridges: H:R.97, H:R.119 Salt bridges: H:R.97, H:R.119, H:K.199, A:K.175 IYP.129: 15 residues within 4Å: Chain D: H.45, H.167, H.168, E.171, K.175 Chain G: R.97, R.119, S.197, S.198, K.199 Chain V: H.71, H.72, E.75 Ligands: MN.127, MN.128 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:R.119, G:S.198 Water bridges: G:R.97, G:R.97 Salt bridges: G:R.97, G:R.119, G:K.199, D:K.175 IYP.135: 15 residues within 4Å: Chain C: H.45, H.167, H.168, E.171, K.175 Chain E: R.97, R.119, S.197, S.198, K.199 Chain W: H.71, H.72, E.75 Ligands: MN.133, MN.134 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:R.119, E:S.198 Water bridges: E:R.97, E:R.97 Salt bridges: E:R.97, E:R.119, E:K.199, C:K.175 IYP.141: 15 residues within 4Å: Chain B: H.45, H.167, H.168, E.171, K.175 Chain F: R.97, R.119, S.197, S.198, K.199 Chain X: H.71, H.72, E.75 Ligands: MN.139, MN.140 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:R.119, F:S.198 Water bridges: F:R.97, F:R.119 Salt bridges: F:R.97, F:R.119, F:K.199, B:K.175

72 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain B: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain B: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain C: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain D: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain D: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain D: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain E: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain E: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain E: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain F: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain F: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain F: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain G: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain G: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain G: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain H: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain H: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain H: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain I: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain I: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain I: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain J: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.59: 6 residues within 4Å: Chain J: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain J: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain K: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain K: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.66: 5 residues within 4Å: Chain K: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.70: 3 residues within 4Å: Chain L: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.71: 6 residues within 4Å: Chain L: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain L: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.76: 3 residues within 4Å: Chain M: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.77: 6 residues within 4Å: Chain M: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.78: 5 residues within 4Å: Chain M: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.82: 3 residues within 4Å: Chain N: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.83: 6 residues within 4Å: Chain N: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.84: 5 residues within 4Å: Chain N: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.88: 3 residues within 4Å: Chain O: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.89: 6 residues within 4Å: Chain O: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.90: 5 residues within 4Å: Chain O: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.94: 3 residues within 4Å: Chain P: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.95: 6 residues within 4Å: Chain P: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.96: 5 residues within 4Å: Chain P: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.100: 3 residues within 4Å: Chain Q: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.101: 6 residues within 4Å: Chain Q: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.102: 5 residues within 4Å: Chain Q: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.106: 3 residues within 4Å: Chain R: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.107: 6 residues within 4Å: Chain R: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.108: 5 residues within 4Å: Chain R: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.112: 3 residues within 4Å: Chain S: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.113: 6 residues within 4Å: Chain S: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.114: 5 residues within 4Å: Chain S: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.118: 3 residues within 4Å: Chain T: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.119: 6 residues within 4Å: Chain T: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.120: 5 residues within 4Å: Chain T: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.124: 3 residues within 4Å: Chain U: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.125: 6 residues within 4Å: Chain U: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.126: 5 residues within 4Å: Chain U: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.130: 3 residues within 4Å: Chain V: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.131: 6 residues within 4Å: Chain V: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.132: 5 residues within 4Å: Chain V: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.136: 3 residues within 4Å: Chain W: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.137: 6 residues within 4Å: Chain W: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.138: 5 residues within 4Å: Chain W: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP EDO.142: 3 residues within 4Å: Chain X: N.125, E.127, Q.160 Ligand excluded by PLIP EDO.143: 6 residues within 4Å: Chain X: N.21, V.22, S.23, R.61, A.62, T.63 Ligand excluded by PLIP EDO.144: 5 residues within 4Å: Chain X: R.9, K.93, G.94, I.95, S.187 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bisson, C. et al., Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination. Structure (2015)

Release Date

2014-09-24

Peptides

Imidazoleglycerol-phosphate dehydratase 2, chloroplastic: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

M
A

N
A

O
A

P
A

Q
A

R
A

S
A

T
A

U
A

V
A

W
A

X
A

Imidazoleglycerol-phosphate dehydratase 2, chloroplastic

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