SMTL ID : 9m2q.1

Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, in complex with aminotriazole

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.80 Å

Oligo State

homo-24-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.79, E.83, H.158 Chain D: H.183 Ligands: 3TR.3 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Metal complexes: D:H.183, A:H.79, A:E.83, A:H.158 MN.2: 5 residues within 4Å: Chain A: H.53, H.182, E.186 Chain B: H.80 Ligands: 3TR.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.53, A:H.182, A:E.186, B:H.80 MN.4: 5 residues within 4Å: Chain A: H.183 Chain B: H.79, E.83, H.158 Ligands: 3TR.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.79, B:E.83, B:H.158, A:H.183 MN.5: 5 residues within 4Å: Chain B: H.53, H.182, E.186 Chain C: H.80 Ligands: 3TR.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.53, B:H.182, B:E.186, C:H.80 MN.7: 5 residues within 4Å: Chain B: H.183 Chain C: H.79, E.83, H.158 Ligands: 3TR.9 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.79, C:E.83, C:H.158, B:H.183 MN.8: 5 residues within 4Å: Chain C: H.53, H.182, E.186 Chain D: H.80 Ligands: 3TR.12 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:H.53, C:H.182, C:E.186, D:H.80 MN.10: 5 residues within 4Å: Chain C: H.183 Chain D: H.79, E.83, H.158 Ligands: 3TR.12 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Metal complexes: C:H.183, D:H.79, D:E.83, D:H.158 MN.11: 5 residues within 4Å: Chain A: H.80 Chain D: H.53, H.182, E.186 Ligands: 3TR.3 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.53, D:H.182, D:E.186, A:H.80 MN.13: 5 residues within 4Å: Chain E: H.79, E.83, H.158 Chain O: H.183 Ligands: 3TR.15 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain O Metal complexes: E:H.79, E:E.83, E:H.158, O:H.183 MN.14: 5 residues within 4Å: Chain E: H.53, H.182, E.186 Chain J: H.80 Ligands: 3TR.30 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain J Metal complexes: E:H.53, E:H.182, E:E.186, J:H.80 MN.16: 5 residues within 4Å: Chain F: H.79, E.83, H.158 Chain L: H.183 Ligands: 3TR.18 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain L Metal complexes: F:H.79, F:E.83, F:H.158, L:H.183 MN.17: 5 residues within 4Å: Chain F: H.53, H.182, E.186 Chain M: H.80 Ligands: 3TR.39 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain M Metal complexes: F:H.53, F:H.182, F:E.186, M:H.80 MN.19: 5 residues within 4Å: Chain G: H.79, E.83, H.158 Chain I: H.183 Ligands: 3TR.21 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain I Metal complexes: G:H.79, G:E.83, G:H.158, I:H.183 MN.20: 5 residues within 4Å: Chain G: H.53, H.182, E.186 Chain P: H.80 Ligands: 3TR.48 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain P Metal complexes: G:H.53, G:H.182, G:E.186, P:H.80 MN.22: 5 residues within 4Å: Chain H: H.79, E.83, H.158 Chain W: H.183 Ligands: 3TR.24 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain W Metal complexes: H:H.79, H:E.83, H:H.158, W:H.183 MN.23: 5 residues within 4Å: Chain H: H.53, H.182, E.186 Chain U: H.80 Ligands: 3TR.63 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain U Metal complexes: H:H.53, H:H.182, H:E.186, U:H.80 MN.25: 5 residues within 4Å: Chain I: H.79, E.83, H.158 Chain R: H.183 Ligands: 3TR.27 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain R Metal complexes: I:H.79, I:E.83, I:H.158, R:H.183 MN.26: 5 residues within 4Å: Chain G: H.80 Chain I: H.53, H.182, E.186 Ligands: 3TR.21 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain G Metal complexes: I:H.53, I:H.182, I:E.186, G:H.80 MN.28: 5 residues within 4Å: Chain E: H.183 Chain J: H.79, E.83, H.158 Ligands: 3TR.30 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain J Metal complexes: E:H.183, J:H.79, J:E.83, J:H.158 MN.29: 5 residues within 4Å: Chain J: H.53, H.182, E.186 Chain S: H.80 Ligands: 3TR.57 4 PLIP interactions: 1 interactions with chain S, 3 interactions with chain J Metal complexes: S:H.80, J:H.53, J:H.182, J:E.186 MN.31: 5 residues within 4Å: Chain K: H.79, E.83, H.158 Chain U: H.183 Ligands: 3TR.33 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain U Metal complexes: K:H.79, K:E.83, K:H.158, U:H.183 MN.32: 5 residues within 4Å: Chain K: H.53, H.182, E.186 Chain W: H.80 Ligands: 3TR.69 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W Metal complexes: K:H.53, K:H.182, K:E.186, W:H.80 MN.34: 5 residues within 4Å: Chain L: H.79, E.83, H.158 Chain T: H.183 Ligands: 3TR.36 4 PLIP interactions: 1 interactions with chain T, 3 interactions with chain L Metal complexes: T:H.183, L:H.79, L:E.83, L:H.158 MN.35: 5 residues within 4Å: Chain F: H.80 Chain L: H.53, H.182, E.186 Ligands: 3TR.18 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain L Metal complexes: F:H.80, L:H.53, L:H.182, L:E.186 MN.37: 5 residues within 4Å: Chain F: H.183 Chain M: H.79, E.83, H.158 Ligands: 3TR.39 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain F Metal complexes: M:H.79, M:E.83, M:H.158, F:H.183 MN.38: 5 residues within 4Å: Chain M: H.53, H.182, E.186 Chain T: H.80 Ligands: 3TR.60 4 PLIP interactions: 1 interactions with chain T, 3 interactions with chain M Metal complexes: T:H.80, M:H.53, M:H.182, M:E.186 MN.40: 5 residues within 4Å: Chain N: H.79, E.83, H.158 Chain V: H.183 Ligands: 3TR.42 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain V Metal complexes: N:H.79, N:E.83, N:H.158, V:H.183 MN.41: 5 residues within 4Å: Chain N: H.53, H.182, E.186 Chain X: H.80 Ligands: 3TR.72 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain X Metal complexes: N:H.53, N:H.182, N:E.186, X:H.80 MN.43: 5 residues within 4Å: Chain O: H.79, E.83, H.158 Chain S: H.183 Ligands: 3TR.45 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain S Metal complexes: O:H.79, O:E.83, O:H.158, S:H.183 MN.44: 5 residues within 4Å: Chain E: H.80 Chain O: H.53, H.182, E.186 Ligands: 3TR.15 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain E Metal complexes: O:H.53, O:H.182, O:E.186, E:H.80 MN.46: 5 residues within 4Å: Chain G: H.183 Chain P: H.79, E.83, H.158 Ligands: 3TR.48 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain G Metal complexes: P:H.79, P:E.83, P:H.158, G:H.183 MN.47: 5 residues within 4Å: Chain P: H.53, H.182, E.186 Chain R: H.80 Ligands: 3TR.54 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain R Metal complexes: P:H.53, P:H.182, P:E.186, R:H.80 MN.49: 5 residues within 4Å: Chain Q: H.79, E.83, H.158 Chain X: H.183 Ligands: 3TR.51 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain X Metal complexes: Q:H.79, Q:E.83, Q:H.158, X:H.183 MN.50: 5 residues within 4Å: Chain Q: H.53, H.182, E.186 Chain V: H.80 Ligands: 3TR.66 4 PLIP interactions: 1 interactions with chain V, 3 interactions with chain Q Metal complexes: V:H.80, Q:H.53, Q:H.182, Q:E.186 MN.52: 5 residues within 4Å: Chain P: H.183 Chain R: H.79, E.83, H.158 Ligands: 3TR.54 4 PLIP interactions: 1 interactions with chain P, 3 interactions with chain R Metal complexes: P:H.183, R:H.79, R:E.83, R:H.158 MN.53: 5 residues within 4Å: Chain I: H.80 Chain R: H.53, H.182, E.186 Ligands: 3TR.27 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain I Metal complexes: R:H.53, R:H.182, R:E.186, I:H.80 MN.55: 5 residues within 4Å: Chain J: H.183 Chain S: H.79, E.83, H.158 Ligands: 3TR.57 4 PLIP interactions: 3 interactions with chain S, 1 interactions with chain J Metal complexes: S:H.79, S:E.83, S:H.158, J:H.183 MN.56: 5 residues within 4Å: Chain O: H.80 Chain S: H.53, H.182, E.186 Ligands: 3TR.45 4 PLIP interactions: 3 interactions with chain S, 1 interactions with chain O Metal complexes: S:H.53, S:H.182, S:E.186, O:H.80 MN.58: 5 residues within 4Å: Chain M: H.183 Chain T: H.79, E.83, H.158 Ligands: 3TR.60 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain M Metal complexes: T:H.79, T:E.83, T:H.158, M:H.183 MN.59: 5 residues within 4Å: Chain L: H.80 Chain T: H.53, H.182, E.186 Ligands: 3TR.36 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain L Metal complexes: T:H.53, T:H.182, T:E.186, L:H.80 MN.61: 5 residues within 4Å: Chain H: H.183 Chain U: H.79, E.83, H.158 Ligands: 3TR.63 4 PLIP interactions: 3 interactions with chain U, 1 interactions with chain H Metal complexes: U:H.79, U:E.83, U:H.158, H:H.183 MN.62: 5 residues within 4Å: Chain K: H.80 Chain U: H.53, H.182, E.186 Ligands: 3TR.33 4 PLIP interactions: 3 interactions with chain U, 1 interactions with chain K Metal complexes: U:H.53, U:H.182, U:E.186, K:H.80 MN.64: 5 residues within 4Å: Chain Q: H.183 Chain V: H.79, E.83, H.158 Ligands: 3TR.66 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain Q Metal complexes: V:H.79, V:E.83, V:H.158, Q:H.183 MN.65: 5 residues within 4Å: Chain N: H.80 Chain V: H.53, H.182, E.186 Ligands: 3TR.42 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain N Metal complexes: V:H.53, V:H.182, V:E.186, N:H.80 MN.67: 5 residues within 4Å: Chain K: H.183 Chain W: H.79, E.83, H.158 Ligands: 3TR.69 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain W Metal complexes: K:H.183, W:H.79, W:E.83, W:H.158 MN.68: 5 residues within 4Å: Chain H: H.80 Chain W: H.53, H.182, E.186 Ligands: 3TR.24 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain W Metal complexes: H:H.80, W:H.53, W:H.182, W:E.186 MN.70: 5 residues within 4Å: Chain N: H.183 Chain X: H.79, E.83, H.158 Ligands: 3TR.72 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain N Metal complexes: X:H.79, X:E.83, X:H.158, N:H.183 MN.71: 5 residues within 4Å: Chain Q: H.80 Chain X: H.53, H.182, E.186 Ligands: 3TR.51 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain Q Metal complexes: X:H.53, X:H.182, X:E.186, Q:H.80

24 x 3TR: 3-AMINO-1,2,4-TRIAZOLE(Non-covalent)

3TR.3: 10 residues within 4Å: Chain A: H.79, H.80, E.83 Chain D: M.113, H.182, H.183, E.186 Chain U: R.127 Ligands: MN.1, MN.11 4 PLIP interactions: 1 interactions with chain U, 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: U:R.127 Salt bridges: D:D.114, D:E.186, A:E.83 3TR.6: 11 residues within 4Å: Chain A: M.113, D.114, H.182, H.183, E.186 Chain B: H.79, H.80, E.83 Chain I: R.127 Ligands: MN.2, MN.4 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain I Salt bridges: B:E.83, A:D.114, A:E.186 Hydrogen bonds: I:R.127 3TR.9: 10 residues within 4Å: Chain B: M.113, H.182, H.183, E.186 Chain C: H.79, H.80, E.83 Chain V: R.127 Ligands: MN.5, MN.7 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain V Salt bridges: B:D.114, B:E.186, C:E.83 Hydrogen bonds: V:R.127 3TR.12: 11 residues within 4Å: Chain C: M.113, D.114, H.182, H.183, E.186 Chain D: H.79, H.80, E.83 Chain J: R.127 Ligands: MN.8, MN.10 4 PLIP interactions: 1 interactions with chain J, 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: J:R.127 Salt bridges: C:D.114, C:E.186, D:E.83 3TR.15: 10 residues within 4Å: Chain E: H.79, H.80, E.83 Chain K: R.127 Chain O: M.113, H.182, H.183, E.186 Ligands: MN.13, MN.44 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain O, 1 interactions with chain K Salt bridges: E:E.83, O:D.114, O:E.186 Hydrogen bonds: O:E.186, K:R.127 3TR.18: 11 residues within 4Å: Chain F: H.79, H.80, E.83 Chain L: M.113, D.114, H.182, H.183, E.186 Chain W: R.127 Ligands: MN.16, MN.35 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain F, 1 interactions with chain W Hydrogen bonds: L:E.186, W:R.127 Salt bridges: L:D.114, L:E.186, F:E.83 3TR.21: 10 residues within 4Å: Chain G: H.79, H.80, E.83 Chain H: R.127 Chain I: M.113, H.182, H.183, E.186 Ligands: MN.19, MN.26 4 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G, 1 interactions with chain H Salt bridges: I:D.114, I:E.186, G:E.83 Hydrogen bonds: H:R.127 3TR.24: 11 residues within 4Å: Chain G: R.127 Chain H: H.79, H.80, E.83 Chain W: M.113, D.114, H.182, H.183, E.186 Ligands: MN.22, MN.68 5 PLIP interactions: 1 interactions with chain H, 3 interactions with chain W, 1 interactions with chain G Salt bridges: H:E.83, W:D.114, W:E.186 Hydrogen bonds: W:E.186, G:R.127 3TR.27: 10 residues within 4Å: Chain B: R.127 Chain I: H.79, H.80, E.83 Chain R: M.113, H.182, H.183, E.186 Ligands: MN.25, MN.53 5 PLIP interactions: 3 interactions with chain R, 1 interactions with chain B, 1 interactions with chain I Hydrogen bonds: R:E.186, B:R.127 Salt bridges: R:D.114, R:E.186, I:E.83 3TR.30: 10 residues within 4Å: Chain D: R.127 Chain E: M.113, H.182, H.183, E.186 Chain J: H.79, H.80, E.83 Ligands: MN.14, MN.28 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D, 1 interactions with chain J Hydrogen bonds: E:E.186, D:R.127 Salt bridges: E:D.114, E:E.186, J:E.83 3TR.33: 11 residues within 4Å: Chain E: R.127 Chain K: H.79, H.80, E.83 Chain U: M.113, D.114, H.182, H.183, E.186 Ligands: MN.31, MN.62 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain K, 3 interactions with chain U Hydrogen bonds: E:R.127, U:E.186 Salt bridges: K:E.83, U:D.114, U:E.186 3TR.36: 11 residues within 4Å: Chain L: H.79, H.80, E.83 Chain P: R.127 Chain T: M.113, D.114, H.182, H.183, E.186 Ligands: MN.34, MN.59 5 PLIP interactions: 3 interactions with chain T, 1 interactions with chain P, 1 interactions with chain L Hydrogen bonds: T:E.186, P:R.127 Salt bridges: T:D.114, T:E.186, L:E.83 3TR.39: 11 residues within 4Å: Chain F: M.113, D.114, H.182, H.183, E.186 Chain M: H.79, H.80, E.83 Chain O: R.127 Ligands: MN.17, MN.37 5 PLIP interactions: 1 interactions with chain M, 3 interactions with chain F, 1 interactions with chain O Salt bridges: M:E.83, F:D.114, F:E.186 Hydrogen bonds: F:E.186, O:R.127 3TR.42: 10 residues within 4Å: Chain N: H.79, H.80, E.83 Chain R: R.127 Chain V: M.113, H.182, H.183, E.186 Ligands: MN.40, MN.65 5 PLIP interactions: 3 interactions with chain V, 1 interactions with chain R, 1 interactions with chain N Hydrogen bonds: V:E.186, R:R.127 Salt bridges: V:D.114, V:E.186, N:E.83 3TR.45: 10 residues within 4Å: Chain M: R.127 Chain O: H.79, H.80, E.83 Chain S: M.113, H.182, H.183, E.186 Ligands: MN.43, MN.56 5 PLIP interactions: 1 interactions with chain M, 3 interactions with chain S, 1 interactions with chain O Hydrogen bonds: M:R.127, S:E.186 Salt bridges: S:D.114, S:E.186, O:E.83 3TR.48: 10 residues within 4Å: Chain G: M.113, H.182, H.183, E.186 Chain L: R.127 Chain P: H.79, H.80, E.83 Ligands: MN.20, MN.46 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain L, 1 interactions with chain P Hydrogen bonds: G:E.186, L:R.127 Salt bridges: G:D.114, G:E.186, P:E.83 3TR.51: 11 residues within 4Å: Chain Q: H.79, H.80, E.83 Chain S: R.127 Chain X: M.113, D.114, H.182, H.183, E.186 Ligands: MN.49, MN.71 5 PLIP interactions: 3 interactions with chain X, 1 interactions with chain S, 1 interactions with chain Q Hydrogen bonds: X:E.186, S:R.127 Salt bridges: X:D.114, X:E.186, Q:E.83 3TR.54: 10 residues within 4Å: Chain N: R.127 Chain P: M.113, H.182, H.183, E.186 Chain R: H.79, H.80, E.83 Ligands: MN.47, MN.52 4 PLIP interactions: 1 interactions with chain N, 2 interactions with chain P, 1 interactions with chain R Hydrogen bonds: N:R.127 Salt bridges: P:D.114, P:E.186, R:E.83 3TR.57: 10 residues within 4Å: Chain J: M.113, H.182, H.183, E.186 Chain Q: R.127 Chain S: H.79, H.80, E.83 Ligands: MN.29, MN.55 5 PLIP interactions: 1 interactions with chain S, 3 interactions with chain J, 1 interactions with chain Q Salt bridges: S:E.83, J:D.114, J:E.186 Hydrogen bonds: J:E.186, Q:R.127 3TR.60: 11 residues within 4Å: Chain M: M.113, D.114, H.182, H.183, E.186 Chain T: H.79, H.80, E.83 Chain X: R.127 Ligands: MN.38, MN.58 5 PLIP interactions: 3 interactions with chain M, 1 interactions with chain X, 1 interactions with chain T Hydrogen bonds: M:E.186, X:R.127 Salt bridges: M:D.114, M:E.186, T:E.83 3TR.63: 10 residues within 4Å: Chain A: R.127 Chain H: M.113, H.182, H.183, E.186 Chain U: H.79, H.80, E.83 Ligands: MN.23, MN.61 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain H, 1 interactions with chain U Hydrogen bonds: A:R.127, H:E.186 Salt bridges: H:D.114, H:E.186, U:E.83 3TR.66: 11 residues within 4Å: Chain C: R.127 Chain Q: M.113, D.114, H.182, H.183, E.186 Chain V: H.79, H.80, E.83 Ligands: MN.50, MN.64 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain Q, 1 interactions with chain V Hydrogen bonds: C:R.127, Q:E.186 Salt bridges: Q:D.114, Q:E.186, V:E.83 3TR.69: 10 residues within 4Å: Chain F: R.127 Chain K: M.113, H.182, H.183, E.186 Chain W: H.79, H.80, E.83 Ligands: MN.32, MN.67 5 PLIP interactions: 1 interactions with chain W, 3 interactions with chain K, 1 interactions with chain F Salt bridges: W:E.83, K:D.114, K:E.186 Hydrogen bonds: K:E.186, F:R.127 3TR.72: 10 residues within 4Å: Chain N: M.113, H.182, H.183, E.186 Chain T: R.127 Chain X: H.79, H.80, E.83 Ligands: MN.41, MN.70 5 PLIP interactions: 3 interactions with chain N, 1 interactions with chain T, 1 interactions with chain X Hydrogen bonds: N:E.186, T:R.127 Salt bridges: N:D.114, N:E.186, X:E.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raina, R. et al., Cryo-EM structures of Mycobacterium tuberculosis imidazole glycerol phosphate dehydratase in the apo state and in the presence of small molecules. Acta Crystallogr.,Sect.F (2025)

Release Date

2025-06-18

Peptides

Imidazoleglycerol-phosphate dehydratase: 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

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