SMTL ID : 6ezj.1

Imidazoleglycerol-phosphate dehydratase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.45, H.167, E.171 Chain Q: H.72 Ligands: 5LD.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain Q Metal complexes: A:H.45, A:H.167, A:E.171, A:E.171, Q:H.72 MN.3: 5 residues within 4Å: Chain A: H.71, E.75, H.143 Chain U: H.168 Ligands: 5LD.63 4 PLIP interactions: 1 interactions with chain U, 3 interactions with chain A Metal complexes: U:H.168, A:H.71, A:E.75, A:H.143 MN.4: 5 residues within 4Å: Chain B: H.45, H.167, E.171 Chain N: H.72 Ligands: 5LD.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain N Metal complexes: B:H.45, B:H.167, B:E.171, B:E.171, N:H.72 MN.6: 5 residues within 4Å: Chain B: H.71, E.75, H.143 Chain F: H.168 Ligands: 5LD.17 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Metal complexes: B:H.71, B:E.75, B:H.143, F:H.168 MN.7: 5 residues within 4Å: Chain C: H.45, H.167, E.171 Chain W: H.72 Ligands: 5LD.8 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain W Metal complexes: C:H.45, C:H.167, C:E.171, C:E.171, W:H.72 MN.9: 5 residues within 4Å: Chain C: H.71, E.75, H.143 Chain S: H.168 Ligands: 5LD.57 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain S Metal complexes: C:H.71, C:E.75, C:H.143, S:H.168 MN.10: 5 residues within 4Å: Chain D: H.45, H.167, E.171 Chain H: H.72 Ligands: 5LD.11 5 PLIP interactions: 1 interactions with chain H, 4 interactions with chain D Metal complexes: H:H.72, D:H.45, D:H.167, D:E.171, D:E.171 MN.12: 5 residues within 4Å: Chain D: H.71, E.75, H.143 Chain X: H.168 Ligands: 5LD.72 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain X Metal complexes: D:H.71, D:E.75, D:H.143, X:H.168 MN.13: 5 residues within 4Å: Chain E: H.45, H.167, E.171 Chain R: H.72 Ligands: 5LD.14 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain R Metal complexes: E:H.45, E:H.167, E:E.171, E:E.171, R:H.72 MN.15: 5 residues within 4Å: Chain E: H.71, E.75, H.143 Chain T: H.168 Ligands: 5LD.60 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain T Metal complexes: E:H.71, E:E.75, E:H.143, T:H.168 MN.16: 5 residues within 4Å: Chain B: H.72 Chain F: H.45, H.167, E.171 Ligands: 5LD.17 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Metal complexes: F:H.45, F:H.167, F:E.171, F:E.171, B:H.72 MN.18: 5 residues within 4Å: Chain F: H.71, E.75, H.143 Chain J: H.168 Ligands: 5LD.29 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain J Metal complexes: F:H.71, F:E.75, F:H.143, J:H.168 MN.19: 5 residues within 4Å: Chain G: H.45, H.167, E.171 Chain V: H.72 Ligands: 5LD.20 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain V Metal complexes: G:H.45, G:H.167, G:E.171, G:E.171, V:H.72 MN.21: 5 residues within 4Å: Chain G: H.71, E.75, H.143 Chain P: H.168 Ligands: 5LD.48 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain P Metal complexes: G:H.71, G:E.75, G:H.143, P:H.168 MN.22: 5 residues within 4Å: Chain D: H.168 Chain H: H.71, E.75, H.143 Ligands: 5LD.11 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain D Metal complexes: H:H.71, H:E.75, H:H.143, D:H.168 MN.23: 5 residues within 4Å: Chain H: H.45, H.167, E.171 Chain L: H.72 Ligands: 5LD.24 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain L Metal complexes: H:H.45, H:H.167, H:E.171, H:E.171, L:H.72 MN.25: 5 residues within 4Å: Chain I: H.45, H.167, E.171 Chain S: H.72 Ligands: 5LD.26 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain S Metal complexes: I:H.45, I:H.167, I:E.171, I:E.171, S:H.72 MN.27: 5 residues within 4Å: Chain I: H.71, E.75, H.143 Chain W: H.168 Ligands: 5LD.69 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain W Metal complexes: I:H.71, I:E.75, I:H.143, W:H.168 MN.28: 5 residues within 4Å: Chain F: H.72 Chain J: H.45, H.167, E.171 Ligands: 5LD.29 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain F Metal complexes: J:H.45, J:H.167, J:E.171, J:E.171, F:H.72 MN.30: 5 residues within 4Å: Chain J: H.71, E.75, H.143 Chain N: H.168 Ligands: 5LD.42 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain J Metal complexes: N:H.168, J:H.71, J:E.75, J:H.143 MN.31: 5 residues within 4Å: Chain K: H.45, H.167, E.171 Chain U: H.72 Ligands: 5LD.32 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain U Metal complexes: K:H.45, K:H.167, K:E.171, K:E.171, U:H.72 MN.33: 5 residues within 4Å: Chain K: H.71, E.75, H.143 Chain Q: H.168 Ligands: 5LD.51 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain Q Metal complexes: K:H.71, K:E.75, K:H.143, Q:H.168 MN.34: 5 residues within 4Å: Chain H: H.168 Chain L: H.71, E.75, H.143 Ligands: 5LD.24 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain L Metal complexes: H:H.168, L:H.71, L:E.75, L:H.143 MN.35: 5 residues within 4Å: Chain L: H.45, H.167, E.171 Chain X: H.72 Ligands: 5LD.36 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain X Metal complexes: L:H.45, L:H.167, L:E.171, L:E.171, X:H.72 MN.37: 5 residues within 4Å: Chain M: H.45, H.167, E.171 Chain P: H.72 Ligands: 5LD.38 5 PLIP interactions: 1 interactions with chain P, 4 interactions with chain M Metal complexes: P:H.72, M:H.45, M:H.167, M:E.171, M:E.171 MN.39: 5 residues within 4Å: Chain M: H.71, E.75, H.143 Chain V: H.168 Ligands: 5LD.66 4 PLIP interactions: 1 interactions with chain V, 3 interactions with chain M Metal complexes: V:H.168, M:H.71, M:E.75, M:H.143 MN.40: 5 residues within 4Å: Chain B: H.168 Chain N: H.71, E.75, H.143 Ligands: 5LD.5 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain B Metal complexes: N:H.71, N:E.75, N:H.143, B:H.168 MN.41: 5 residues within 4Å: Chain J: H.72 Chain N: H.45, H.167, E.171 Ligands: 5LD.42 5 PLIP interactions: 1 interactions with chain J, 4 interactions with chain N Metal complexes: J:H.72, N:H.45, N:H.167, N:E.171, N:E.171 MN.43: 5 residues within 4Å: Chain O: H.45, H.167, E.171 Chain T: H.72 Ligands: 5LD.44 5 PLIP interactions: 4 interactions with chain O, 1 interactions with chain T Metal complexes: O:H.45, O:H.167, O:E.171, O:E.171, T:H.72 MN.45: 5 residues within 4Å: Chain O: H.71, E.75, H.143 Chain R: H.168 Ligands: 5LD.54 4 PLIP interactions: 1 interactions with chain R, 3 interactions with chain O Metal complexes: R:H.168, O:H.71, O:E.75, O:H.143 MN.46: 5 residues within 4Å: Chain M: H.168 Chain P: H.71, E.75, H.143 Ligands: 5LD.38 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain M Metal complexes: P:H.71, P:E.75, P:H.143, M:H.168 MN.47: 5 residues within 4Å: Chain G: H.72 Chain P: H.45, H.167, E.171 Ligands: 5LD.48 5 PLIP interactions: 4 interactions with chain P, 1 interactions with chain G Metal complexes: P:H.45, P:H.167, P:E.171, P:E.171, G:H.72 MN.49: 5 residues within 4Å: Chain A: H.168 Chain Q: H.71, E.75, H.143 Ligands: 5LD.2 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain A Metal complexes: Q:H.71, Q:E.75, Q:H.143, A:H.168 MN.50: 5 residues within 4Å: Chain K: H.72 Chain Q: H.45, H.167, E.171 Ligands: 5LD.51 5 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain K Metal complexes: Q:H.45, Q:H.167, Q:E.171, Q:E.171, K:H.72 MN.52: 5 residues within 4Å: Chain E: H.168 Chain R: H.71, E.75, H.143 Ligands: 5LD.14 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain E Metal complexes: R:H.71, R:E.75, R:H.143, E:H.168 MN.53: 5 residues within 4Å: Chain O: H.72 Chain R: H.45, H.167, E.171 Ligands: 5LD.54 5 PLIP interactions: 4 interactions with chain R, 1 interactions with chain O Metal complexes: R:H.45, R:H.167, R:E.171, R:E.171, O:H.72 MN.55: 5 residues within 4Å: Chain I: H.168 Chain S: H.71, E.75, H.143 Ligands: 5LD.26 4 PLIP interactions: 3 interactions with chain S, 1 interactions with chain I Metal complexes: S:H.71, S:E.75, S:H.143, I:H.168 MN.56: 5 residues within 4Å: Chain C: H.72 Chain S: H.45, H.167, E.171 Ligands: 5LD.57 5 PLIP interactions: 4 interactions with chain S, 1 interactions with chain C Metal complexes: S:H.45, S:H.167, S:E.171, S:E.171, C:H.72 MN.58: 5 residues within 4Å: Chain O: H.168 Chain T: H.71, E.75, H.143 Ligands: 5LD.44 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain O Metal complexes: T:H.71, T:E.75, T:H.143, O:H.168 MN.59: 5 residues within 4Å: Chain E: H.72 Chain T: H.45, H.167, E.171 Ligands: 5LD.60 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain T Metal complexes: E:H.72, T:H.45, T:H.167, T:E.171, T:E.171 MN.61: 5 residues within 4Å: Chain K: H.168 Chain U: H.71, E.75, H.143 Ligands: 5LD.32 4 PLIP interactions: 3 interactions with chain U, 1 interactions with chain K Metal complexes: U:H.71, U:E.75, U:H.143, K:H.168 MN.62: 5 residues within 4Å: Chain A: H.72 Chain U: H.45, H.167, E.171 Ligands: 5LD.63 5 PLIP interactions: 4 interactions with chain U, 1 interactions with chain A Metal complexes: U:H.45, U:H.167, U:E.171, U:E.171, A:H.72 MN.64: 5 residues within 4Å: Chain G: H.168 Chain V: H.71, E.75, H.143 Ligands: 5LD.20 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain G Metal complexes: V:H.71, V:E.75, V:H.143, G:H.168 MN.65: 5 residues within 4Å: Chain M: H.72 Chain V: H.45, H.167, E.171 Ligands: 5LD.66 5 PLIP interactions: 4 interactions with chain V, 1 interactions with chain M Metal complexes: V:H.45, V:H.167, V:E.171, V:E.171, M:H.72 MN.67: 5 residues within 4Å: Chain C: H.168 Chain W: H.71, E.75, H.143 Ligands: 5LD.8 4 PLIP interactions: 3 interactions with chain W, 1 interactions with chain C Metal complexes: W:H.71, W:E.75, W:H.143, C:H.168 MN.68: 5 residues within 4Å: Chain I: H.72 Chain W: H.45, H.167, E.171 Ligands: 5LD.69 5 PLIP interactions: 4 interactions with chain W, 1 interactions with chain I Metal complexes: W:H.45, W:H.167, W:E.171, W:E.171, I:H.72 MN.70: 5 residues within 4Å: Chain L: H.168 Chain X: H.71, E.75, H.143 Ligands: 5LD.36 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain L Metal complexes: X:H.71, X:E.75, X:H.143, L:H.168 MN.71: 5 residues within 4Å: Chain D: H.72 Chain X: H.45, H.167, E.171 Ligands: 5LD.72 5 PLIP interactions: 4 interactions with chain X, 1 interactions with chain D Metal complexes: X:H.45, X:H.167, X:E.171, X:E.171, D:H.72

24 x 5LD: [(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid(Non-covalent)

5LD.2: 14 residues within 4Å: Chain A: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain Q: H.71, H.72, E.75 Chain V: R.97, R.119 Ligands: MN.1, MN.49 4 PLIP interactions: 2 interactions with chain V, 2 interactions with chain A Hydrogen bonds: V:R.97, V:R.119, A:Q.49, A:K.175 5LD.5: 14 residues within 4Å: Chain B: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain G: R.97, R.119 Chain N: H.71, H.72, E.75 Ligands: MN.4, MN.40 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain G Hydrogen bonds: B:Q.49, B:K.175, G:R.97, G:R.119 5LD.8: 14 residues within 4Å: Chain C: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain P: R.97, R.119 Chain W: H.71, H.72, E.75 Ligands: MN.7, MN.67 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain P Hydrogen bonds: C:Q.49, C:K.175, P:R.97, P:R.119 5LD.11: 14 residues within 4Å: Chain A: R.97, R.119 Chain D: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain H: H.71, H.72, E.75 Ligands: MN.10, MN.22 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Q.49, D:K.175, A:R.97, A:R.119 5LD.14: 14 residues within 4Å: Chain E: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain R: H.71, H.72, E.75 Chain U: R.97, R.119 Ligands: MN.13, MN.52 4 PLIP interactions: 2 interactions with chain U, 2 interactions with chain E Hydrogen bonds: U:R.97, U:R.119, E:Q.49, E:K.175 5LD.17: 14 residues within 4Å: Chain B: H.71, H.72, E.75 Chain F: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain K: R.97, R.119 Ligands: MN.6, MN.16 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain K Hydrogen bonds: F:Q.49, F:K.175, K:R.97, K:R.119 5LD.20: 13 residues within 4Å: Chain G: Q.49, L.105, H.167, H.168, E.171, K.175 Chain Q: R.97, R.119 Chain V: H.71, H.72, E.75 Ligands: MN.19, MN.64 4 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain G Hydrogen bonds: Q:R.97, Q:R.119, G:Q.49, G:K.175 5LD.24: 14 residues within 4Å: Chain E: R.97, R.119 Chain H: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain L: H.71, H.72, E.75 Ligands: MN.23, MN.34 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain E Hydrogen bonds: H:Q.49, H:K.175, E:R.97, E:R.119 5LD.26: 14 residues within 4Å: Chain I: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain S: H.71, H.72, E.75 Chain T: R.97, R.119 Ligands: MN.25, MN.55 4 PLIP interactions: 2 interactions with chain T, 2 interactions with chain I Hydrogen bonds: T:R.97, T:R.119, I:Q.49, I:K.175 5LD.29: 14 residues within 4Å: Chain F: H.71, H.72, E.75 Chain J: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain O: R.97, R.119 Ligands: MN.18, MN.28 4 PLIP interactions: 2 interactions with chain O, 2 interactions with chain J Hydrogen bonds: O:R.97, O:R.119, J:Q.49, J:K.175 5LD.32: 13 residues within 4Å: Chain K: Q.49, L.105, H.167, H.168, E.171, K.175 Chain R: R.97, R.119 Chain U: H.71, H.72, E.75 Ligands: MN.31, MN.61 4 PLIP interactions: 2 interactions with chain R, 2 interactions with chain K Hydrogen bonds: R:R.97, R:R.119, K:Q.49, K:K.175 5LD.36: 14 residues within 4Å: Chain I: R.97, R.119 Chain L: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain X: H.71, H.72, E.75 Ligands: MN.35, MN.70 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain L Hydrogen bonds: I:R.97, I:R.119, L:Q.49, L:K.175 5LD.38: 14 residues within 4Å: Chain M: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain P: H.71, H.72, E.75 Chain W: R.97, R.119 Ligands: MN.37, MN.46 4 PLIP interactions: 2 interactions with chain W, 2 interactions with chain M Hydrogen bonds: W:R.97, W:R.119, M:Q.49, M:K.175 5LD.42: 14 residues within 4Å: Chain C: R.97, R.119 Chain J: H.71, H.72, E.75 Chain N: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.30, MN.41 4 PLIP interactions: 2 interactions with chain N, 2 interactions with chain C Hydrogen bonds: N:Q.49, N:K.175, C:R.97, C:R.119 5LD.44: 14 residues within 4Å: Chain O: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain S: R.97, R.119 Chain T: H.71, H.72, E.75 Ligands: MN.43, MN.58 4 PLIP interactions: 2 interactions with chain S, 2 interactions with chain O Hydrogen bonds: S:R.97, S:R.119, O:Q.49, O:K.175 5LD.48: 14 residues within 4Å: Chain G: H.71, H.72, E.75 Chain N: R.97, R.119 Chain P: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.21, MN.47 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain N Hydrogen bonds: P:Q.49, P:K.175, N:R.97, N:R.119 5LD.51: 14 residues within 4Å: Chain B: R.97, R.119 Chain K: H.71, H.72, E.75 Chain Q: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.33, MN.50 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain Q Hydrogen bonds: B:R.97, B:R.119, Q:Q.49, Q:K.175 5LD.54: 14 residues within 4Å: Chain F: R.97, R.119 Chain O: H.71, H.72, E.75 Chain R: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.45, MN.53 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain R Hydrogen bonds: F:R.97, F:R.119, R:Q.49, R:K.175 5LD.57: 14 residues within 4Å: Chain C: H.71, H.72, E.75 Chain J: R.97, R.119 Chain S: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.9, MN.56 4 PLIP interactions: 2 interactions with chain S, 2 interactions with chain J Hydrogen bonds: S:Q.49, S:K.175, J:R.97, J:R.119 5LD.60: 14 residues within 4Å: Chain E: H.71, H.72, E.75 Chain L: R.97, R.119 Chain T: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.15, MN.59 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain T Hydrogen bonds: L:R.97, L:R.119, T:Q.49, T:K.175 5LD.63: 13 residues within 4Å: Chain A: H.71, H.72, E.75 Chain H: R.97, R.119 Chain U: Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.3, MN.62 4 PLIP interactions: 2 interactions with chain U, 2 interactions with chain H Hydrogen bonds: U:Q.49, U:K.175, H:R.97, H:R.119 5LD.66: 14 residues within 4Å: Chain D: R.97, R.119 Chain M: H.71, H.72, E.75 Chain V: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.39, MN.65 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain V Hydrogen bonds: D:R.97, D:R.119, V:Q.49, V:K.175 5LD.69: 14 residues within 4Å: Chain I: H.71, H.72, E.75 Chain W: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Chain X: R.97, R.119 Ligands: MN.27, MN.68 4 PLIP interactions: 2 interactions with chain W, 2 interactions with chain X Hydrogen bonds: W:Q.49, W:K.175, X:R.97, X:R.119 5LD.72: 14 residues within 4Å: Chain D: H.71, H.72, E.75 Chain M: R.97, R.119 Chain X: H.45, Q.49, L.105, H.167, H.168, E.171, K.175 Ligands: MN.12, MN.71 4 PLIP interactions: 2 interactions with chain X, 2 interactions with chain M Hydrogen bonds: X:Q.49, X:K.175, M:R.97, M:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rawson, S. et al., Elucidating the structural basis for differing enzyme inhibitor potency by cryo-EM. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-02-07

Peptides

Imidazoleglycerol-phosphate dehydratase 2, chloroplastic: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Imidazoleglycerol-phosphate dehydratase 2, chloroplastic

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