SMTL ID : 6khh.1

Crystal Structure of HisB from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-24-mer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.64, E.68, H.143 Chain P: H.168 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain P, 2 Ligand-Water interactions Metal complexes: A:H.64, A:E.68, A:H.143, P:H.168, H2O.1, H2O.6 MN.2: 4 residues within 4Å: Chain A: H.38, H.167, E.171 Chain O: H.65 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: A:H.38, A:H.167, A:E.171, O:H.65, H2O.2, H2O.106 MN.5: 4 residues within 4Å: Chain B: H.64, E.68, H.143 Chain O: H.168 6 PLIP interactions: 3 interactions with chain B, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: B:H.64, B:E.68, B:H.143, O:H.168, H2O.9, H2O.13 MN.6: 4 residues within 4Å: Chain B: H.38, H.167, E.171 Chain P: H.65 6 PLIP interactions: 3 interactions with chain B, 1 interactions with chain P, 2 Ligand-Water interactions Metal complexes: B:H.38, B:H.167, B:E.171, P:H.65, H2O.10, H2O.113 MN.9: 4 residues within 4Å: Chain C: H.64, E.68, H.143 Chain M: H.168 6 PLIP interactions: 1 interactions with chain M, 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: M:H.168, C:H.64, C:E.68, C:H.143, H2O.16, H2O.20 MN.10: 4 residues within 4Å: Chain C: H.38, H.167, E.171 Chain N: H.65 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain N, 2 Ligand-Water interactions Metal complexes: C:H.38, C:H.167, C:E.171, N:H.65, H2O.17, H2O.99 MN.13: 4 residues within 4Å: Chain D: H.64, E.68, H.143 Chain N: H.168 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain N, 2 Ligand-Water interactions Metal complexes: D:H.64, D:E.68, D:H.143, N:H.168, H2O.23, H2O.27 MN.14: 4 residues within 4Å: Chain D: H.38, H.167, E.171 Chain M: H.65 6 PLIP interactions: 1 interactions with chain M, 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: M:H.65, D:H.38, D:H.167, D:E.171, H2O.24, H2O.92 MN.17: 4 residues within 4Å: Chain E: H.64, E.68, H.143 Chain V: H.168 6 PLIP interactions: 3 interactions with chain E, 1 interactions with chain V, 2 Ligand-Water interactions Metal complexes: E:H.64, E:E.68, E:H.143, V:H.168, H2O.30, H2O.35 MN.18: 4 residues within 4Å: Chain E: H.38, H.167, E.171 Chain U: H.65 6 PLIP interactions: 3 interactions with chain E, 1 interactions with chain U, 2 Ligand-Water interactions Metal complexes: E:H.38, E:H.167, E:E.171, U:H.65, H2O.31, H2O.149 MN.21: 4 residues within 4Å: Chain F: H.64, E.68, H.143 Chain U: H.168 6 PLIP interactions: 3 interactions with chain F, 1 interactions with chain U, 2 Ligand-Water interactions Metal complexes: F:H.64, F:E.68, F:H.143, U:H.168, H2O.37, H2O.42 MN.22: 4 residues within 4Å: Chain F: H.38, H.167, E.171 Chain V: H.65 6 PLIP interactions: 3 interactions with chain F, 1 interactions with chain V, 2 Ligand-Water interactions Metal complexes: F:H.38, F:H.167, F:E.171, V:H.65, H2O.38, H2O.156 MN.25: 4 residues within 4Å: Chain G: H.64, E.68, H.143 Chain W: H.168 6 PLIP interactions: 3 interactions with chain G, 1 interactions with chain W, 2 Ligand-Water interactions Metal complexes: G:H.64, G:E.68, G:H.143, W:H.168, H2O.44, H2O.49 MN.26: 4 residues within 4Å: Chain G: H.38, H.167, E.171 Chain X: H.65 6 PLIP interactions: 3 interactions with chain G, 1 interactions with chain X, 2 Ligand-Water interactions Metal complexes: G:H.38, G:H.167, G:E.171, X:H.65, H2O.45, H2O.171 MN.29: 4 residues within 4Å: Chain H: H.64, E.68, H.143 Chain X: H.168 6 PLIP interactions: 3 interactions with chain H, 1 interactions with chain X, 2 Ligand-Water interactions Metal complexes: H:H.64, H:E.68, H:H.143, X:H.168, H2O.52, H2O.56 MN.30: 4 residues within 4Å: Chain H: H.38, H.167, E.171 Chain W: H.65 6 PLIP interactions: 3 interactions with chain H, 1 interactions with chain W, 2 Ligand-Water interactions Metal complexes: H:H.38, H:H.167, H:E.171, W:H.65, H2O.53, H2O.163 MN.33: 4 residues within 4Å: Chain I: H.64, E.68, H.143 Chain Q: H.168 6 PLIP interactions: 3 interactions with chain I, 1 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: I:H.64, I:E.68, I:H.143, Q:H.168, H2O.59, H2O.63 MN.34: 4 residues within 4Å: Chain I: H.38, H.167, E.171 Chain R: H.65 6 PLIP interactions: 3 interactions with chain I, 1 interactions with chain R, 2 Ligand-Water interactions Metal complexes: I:H.38, I:H.167, I:E.171, R:H.65, H2O.60, H2O.128 MN.37: 4 residues within 4Å: Chain J: H.64, E.68, H.143 Chain R: H.168 6 PLIP interactions: 3 interactions with chain J, 1 interactions with chain R, 2 Ligand-Water interactions Metal complexes: J:H.64, J:E.68, J:H.143, R:H.168, H2O.66, H2O.70 MN.38: 4 residues within 4Å: Chain J: H.38, H.167, E.171 Chain Q: H.65 6 PLIP interactions: 3 interactions with chain J, 1 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: J:H.38, J:H.167, J:E.171, Q:H.65, H2O.67, H2O.120 MN.41: 4 residues within 4Å: Chain K: H.64, E.68, H.143 Chain T: H.168 6 PLIP interactions: 1 interactions with chain T, 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: T:H.168, K:H.64, K:E.68, K:H.143, H2O.73, H2O.77 MN.42: 4 residues within 4Å: Chain K: H.38, H.167, E.171 Chain S: H.65 6 PLIP interactions: 1 interactions with chain S, 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: S:H.65, K:H.38, K:H.167, K:E.171, H2O.74, H2O.135 MN.45: 4 residues within 4Å: Chain L: H.64, E.68, H.143 Chain S: H.168 6 PLIP interactions: 3 interactions with chain L, 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: L:H.64, L:E.68, L:H.143, S:H.168, H2O.80, H2O.85 MN.46: 4 residues within 4Å: Chain L: H.38, H.167, E.171 Chain T: H.65 6 PLIP interactions: 3 interactions with chain L, 1 interactions with chain T, 2 Ligand-Water interactions Metal complexes: L:H.38, L:H.167, L:E.171, T:H.65, H2O.81, H2O.142 MN.49: 4 residues within 4Å: Chain D: H.168 Chain M: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain M, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: M:H.64, M:E.68, M:H.143, D:H.168, H2O.87, H2O.92 MN.50: 4 residues within 4Å: Chain C: H.65 Chain M: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain M, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: M:H.38, M:H.167, M:E.171, C:H.65, H2O.20, H2O.88 MN.53: 4 residues within 4Å: Chain C: H.168 Chain N: H.64, E.68, H.143 6 PLIP interactions: 1 interactions with chain C, 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: C:H.168, N:H.64, N:E.68, N:H.143, H2O.94, H2O.99 MN.54: 4 residues within 4Å: Chain D: H.65 Chain N: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain N, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: N:H.38, N:H.167, N:E.171, D:H.65, H2O.27, H2O.95 MN.57: 4 residues within 4Å: Chain A: H.168 Chain O: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain O, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: O:H.64, O:E.68, O:H.143, A:H.168, H2O.102, H2O.106 MN.58: 4 residues within 4Å: Chain B: H.65 Chain O: H.38, H.167, E.171 6 PLIP interactions: 1 interactions with chain B, 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: B:H.65, O:H.38, O:H.167, O:E.171, H2O.13, H2O.103 MN.61: 4 residues within 4Å: Chain B: H.168 Chain P: H.64, E.68, H.143 6 PLIP interactions: 1 interactions with chain B, 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: B:H.168, P:H.64, P:E.68, P:H.143, H2O.109, H2O.113 MN.62: 4 residues within 4Å: Chain A: H.65 Chain P: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain P, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: P:H.38, P:H.167, P:E.171, A:H.65, H2O.6, H2O.110 MN.65: 4 residues within 4Å: Chain J: H.168 Chain Q: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: Q:H.64, Q:E.68, Q:H.143, J:H.168, H2O.116, H2O.120 MN.66: 4 residues within 4Å: Chain I: H.65 Chain Q: H.38, H.167, E.171 6 PLIP interactions: 1 interactions with chain I, 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: I:H.65, Q:H.38, Q:H.167, Q:E.171, H2O.63, H2O.117 MN.69: 4 residues within 4Å: Chain I: H.168 Chain R: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain R, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: R:H.64, R:E.68, R:H.143, I:H.168, H2O.123, H2O.128 MN.70: 4 residues within 4Å: Chain J: H.65 Chain R: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain R, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: R:H.38, R:H.167, R:E.171, J:H.65, H2O.70, H2O.124 MN.73: 4 residues within 4Å: Chain K: H.168 Chain S: H.64, E.68, H.143 6 PLIP interactions: 1 interactions with chain K, 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: K:H.168, S:H.64, S:E.68, S:H.143, H2O.130, H2O.135 MN.74: 4 residues within 4Å: Chain L: H.65 Chain S: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain S, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: S:H.38, S:H.167, S:E.171, L:H.65, H2O.85, H2O.131 MN.77: 4 residues within 4Å: Chain L: H.168 Chain T: H.64, E.68, H.143 6 PLIP interactions: 1 interactions with chain L, 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: L:H.168, T:H.64, T:E.68, T:H.143, H2O.137, H2O.142 MN.78: 4 residues within 4Å: Chain K: H.65 Chain T: H.38, H.167, E.171 6 PLIP interactions: 1 interactions with chain K, 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: K:H.65, T:H.38, T:H.167, T:E.171, H2O.78, H2O.138 MN.81: 4 residues within 4Å: Chain E: H.168 Chain U: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain U, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: U:H.64, U:E.68, U:H.143, E:H.168, H2O.145, H2O.149 MN.82: 4 residues within 4Å: Chain F: H.65 Chain U: H.38, H.167, E.171 6 PLIP interactions: 1 interactions with chain F, 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: F:H.65, U:H.38, U:H.167, U:E.171, H2O.42, H2O.146 MN.85: 4 residues within 4Å: Chain F: H.168 Chain V: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain V, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: V:H.64, V:E.68, V:H.143, F:H.168, H2O.152, H2O.156 MN.86: 4 residues within 4Å: Chain E: H.65 Chain V: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain V, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: V:H.38, V:H.167, V:E.171, E:H.65, H2O.35, H2O.153 MN.89: 4 residues within 4Å: Chain H: H.168 Chain W: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain W, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: W:H.64, W:E.68, W:H.143, H:H.168, H2O.159, H2O.163 MN.90: 4 residues within 4Å: Chain G: H.65 Chain W: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain W, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: W:H.38, W:H.167, W:E.171, G:H.65, H2O.49, H2O.160 MN.93: 4 residues within 4Å: Chain G: H.168 Chain X: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain X, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: X:H.64, X:E.68, X:H.143, G:H.168, H2O.166, H2O.170 MN.94: 4 residues within 4Å: Chain H: H.65 Chain X: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain X, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: X:H.38, X:H.167, X:E.171, H:H.65, H2O.56, H2O.167

24 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 8 residues within 4Å: Chain A: F.95, R.159 Chain G: F.95, R.159 Chain J: F.95, R.159 Ligands: CL.27, CL.39 Ligand excluded by PLIP CL.7: 8 residues within 4Å: Chain B: F.95, R.159 Chain E: F.95, R.159 Chain K: F.95, R.159 Ligands: CL.19, CL.43 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain C: F.95, R.159 Chain F: F.95, R.159 Chain I: F.95, R.159 Ligands: CL.23, CL.35 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain D: F.95, R.159 Chain H: F.95, R.159 Chain L: F.95, R.159 Ligands: CL.31, CL.47 Ligand excluded by PLIP CL.19: 8 residues within 4Å: Chain B: F.95, R.159 Chain E: F.95, R.159 Chain K: F.95, R.159 Ligands: CL.7, CL.43 Ligand excluded by PLIP CL.23: 8 residues within 4Å: Chain C: F.95, R.159 Chain F: F.95, R.159 Chain I: F.95, R.159 Ligands: CL.11, CL.35 Ligand excluded by PLIP CL.27: 8 residues within 4Å: Chain A: F.95, R.159 Chain G: F.95, R.159 Chain J: F.95, R.159 Ligands: CL.3, CL.39 Ligand excluded by PLIP CL.31: 8 residues within 4Å: Chain D: F.95, R.159 Chain H: F.95, R.159 Chain L: F.95, R.159 Ligands: CL.15, CL.47 Ligand excluded by PLIP CL.35: 8 residues within 4Å: Chain C: F.95, R.159 Chain F: F.95, R.159 Chain I: F.95, R.159 Ligands: CL.11, CL.23 Ligand excluded by PLIP CL.39: 8 residues within 4Å: Chain A: F.95, R.159 Chain G: F.95, R.159 Chain J: F.95, R.159 Ligands: CL.3, CL.27 Ligand excluded by PLIP CL.43: 8 residues within 4Å: Chain B: F.95, R.159 Chain E: F.95, R.159 Chain K: F.95, R.159 Ligands: CL.7, CL.19 Ligand excluded by PLIP CL.47: 8 residues within 4Å: Chain D: F.95, R.159 Chain H: F.95, R.159 Chain L: F.95, R.159 Ligands: CL.15, CL.31 Ligand excluded by PLIP CL.51: 8 residues within 4Å: Chain M: F.95, R.159 Chain S: F.95, R.159 Chain V: F.95, R.159 Ligands: CL.75, CL.87 Ligand excluded by PLIP CL.55: 8 residues within 4Å: Chain N: F.95, R.159 Chain Q: F.95, R.159 Chain W: F.95, R.159 Ligands: CL.67, CL.91 Ligand excluded by PLIP CL.59: 8 residues within 4Å: Chain O: F.95, R.159 Chain R: F.95, R.159 Chain U: F.95, R.159 Ligands: CL.71, CL.83 Ligand excluded by PLIP CL.63: 8 residues within 4Å: Chain P: F.95, R.159 Chain T: F.95, R.159 Chain X: F.95, R.159 Ligands: CL.79, CL.95 Ligand excluded by PLIP CL.67: 8 residues within 4Å: Chain N: F.95, R.159 Chain Q: F.95, R.159 Chain W: F.95, R.159 Ligands: CL.55, CL.91 Ligand excluded by PLIP CL.71: 8 residues within 4Å: Chain O: F.95, R.159 Chain R: F.95, R.159 Chain U: F.95, R.159 Ligands: CL.59, CL.83 Ligand excluded by PLIP CL.75: 8 residues within 4Å: Chain M: F.95, R.159 Chain S: F.95, R.159 Chain V: F.95, R.159 Ligands: CL.51, CL.87 Ligand excluded by PLIP CL.79: 8 residues within 4Å: Chain P: F.95, R.159 Chain T: F.95, R.159 Chain X: F.95, R.159 Ligands: CL.63, CL.95 Ligand excluded by PLIP CL.83: 8 residues within 4Å: Chain O: F.95, R.159 Chain R: F.95, R.159 Chain U: F.95, R.159 Ligands: CL.59, CL.71 Ligand excluded by PLIP CL.87: 8 residues within 4Å: Chain M: F.95, R.159 Chain S: F.95, R.159 Chain V: F.95, R.159 Ligands: CL.51, CL.75 Ligand excluded by PLIP CL.91: 8 residues within 4Å: Chain N: F.95, R.159 Chain Q: F.95, R.159 Chain W: F.95, R.159 Ligands: CL.55, CL.67 Ligand excluded by PLIP CL.95: 8 residues within 4Å: Chain P: F.95, R.159 Chain T: F.95, R.159 Chain X: F.95, R.159 Ligands: CL.63, CL.79 Ligand excluded by PLIP

24 x ACM: ACETAMIDE(Non-covalent)

ACM.4: 3 residues within 4Å: Chain A: H.46, K.175 Chain J: R.90 Ligand excluded by PLIP ACM.8: 3 residues within 4Å: Chain B: H.46, K.175 Chain K: R.90 Ligand excluded by PLIP ACM.12: 3 residues within 4Å: Chain C: H.46, K.175 Chain I: R.90 Ligand excluded by PLIP ACM.16: 3 residues within 4Å: Chain D: H.46, K.175 Chain L: R.90 Ligand excluded by PLIP ACM.20: 3 residues within 4Å: Chain B: R.90 Chain E: H.46, K.175 Ligand excluded by PLIP ACM.24: 3 residues within 4Å: Chain C: R.90 Chain F: H.46, K.175 Ligand excluded by PLIP ACM.28: 3 residues within 4Å: Chain A: R.90 Chain G: H.46, K.175 Ligand excluded by PLIP ACM.32: 3 residues within 4Å: Chain D: R.90 Chain H: H.46, K.175 Ligand excluded by PLIP ACM.36: 3 residues within 4Å: Chain F: R.90 Chain I: H.46, K.175 Ligand excluded by PLIP ACM.40: 3 residues within 4Å: Chain G: R.90 Chain J: H.46, K.175 Ligand excluded by PLIP ACM.44: 3 residues within 4Å: Chain E: R.90 Chain K: H.46, K.175 Ligand excluded by PLIP ACM.48: 3 residues within 4Å: Chain H: R.90 Chain L: H.46, K.175 Ligand excluded by PLIP ACM.52: 3 residues within 4Å: Chain M: H.46, K.175 Chain V: R.90 Ligand excluded by PLIP ACM.56: 3 residues within 4Å: Chain N: H.46, K.175 Chain W: R.90 Ligand excluded by PLIP ACM.60: 3 residues within 4Å: Chain O: H.46, K.175 Chain U: R.90 Ligand excluded by PLIP ACM.64: 3 residues within 4Å: Chain P: H.46, K.175 Chain X: R.90 Ligand excluded by PLIP ACM.68: 3 residues within 4Å: Chain N: R.90 Chain Q: H.46, K.175 Ligand excluded by PLIP ACM.72: 3 residues within 4Å: Chain O: R.90 Chain R: H.46, K.175 Ligand excluded by PLIP ACM.76: 3 residues within 4Å: Chain M: R.90 Chain S: H.46, K.175 Ligand excluded by PLIP ACM.80: 3 residues within 4Å: Chain P: R.90 Chain T: H.46, K.175 Ligand excluded by PLIP ACM.84: 3 residues within 4Å: Chain R: R.90 Chain U: H.46, K.175 Ligand excluded by PLIP ACM.88: 3 residues within 4Å: Chain S: R.90 Chain V: H.46, K.175 Ligand excluded by PLIP ACM.92: 3 residues within 4Å: Chain Q: R.90 Chain W: H.46, K.175 Ligand excluded by PLIP ACM.96: 3 residues within 4Å: Chain T: R.90 Chain X: H.46, K.175 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, D. et al., Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol-phosphate dehydratase. Proteins (2021)

Release Date

2020-07-15

Peptides

Imidazoleglycerol-phosphate dehydratase: 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

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