SMTL ID : 6yjh.1

Crystal structure of Imidazole Glycerol Phosphate Dehydratase from Mycobacterium tuberculosis at 1.61 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-23-mer

Ligands

69 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.2, H2O.4 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.4 MN.3: 5 residues within 4Å: Chain A: R.159 Chain G: R.159 Chain J: R.159 Ligands: MN.21, MN.30 No protein-ligand interaction detected (PLIP) MN.4: 4 residues within 4Å: Chain B: H.64, E.68, H.143 Chain O: H.168 6 PLIP interactions: 1 interactions with chain O, 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: O:H.168, B:H.64, B:E.68, B:H.143, H2O.5, H2O.7 MN.5: 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.5, H2O.8 MN.6: 5 residues within 4Å: Chain B: R.159 Chain E: R.159 Chain K: R.159 Ligands: MN.15, MN.33 No protein-ligand interaction detected (PLIP) MN.7: 4 residues within 4Å: Chain C: H.64, E.68, H.143 Chain M: H.168 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain M, 2 Ligand-Water interactions Metal complexes: C:H.64, C:E.68, C:H.143, M:H.168, H2O.9, H2O.11 MN.8: 4 residues within 4Å: Chain C: H.38, H.167, E.171 Chain N: H.65 6 PLIP interactions: 1 interactions with chain N, 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: N:H.65, C:H.38, C:H.167, C:E.171, H2O.9, H2O.11 MN.9: 5 residues within 4Å: Chain C: R.159 Chain F: R.159 Chain I: R.159 Ligands: MN.18, MN.27 No protein-ligand interaction detected (PLIP) MN.10: 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.13, H2O.15 MN.11: 4 residues within 4Å: Chain D: H.38, H.167, E.171 Chain M: H.65 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain M, 2 Ligand-Water interactions Metal complexes: D:H.38, D:H.167, D:E.171, M:H.65, H2O.13, H2O.15 MN.12: 5 residues within 4Å: Chain D: R.159 Chain H: R.159 Chain L: R.159 Ligands: MN.24, MN.36 No protein-ligand interaction detected (PLIP) MN.13: 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.17, H2O.19 MN.14: 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.17, H2O.19 MN.15: 5 residues within 4Å: Chain B: R.159 Chain E: R.159 Chain K: R.159 Ligands: MN.6, MN.33 No protein-ligand interaction detected (PLIP) MN.16: 4 residues within 4Å: Chain F: H.64, E.68, H.143 Chain U: H.168 6 PLIP interactions: 1 interactions with chain U, 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: U:H.168, F:H.64, F:E.68, F:H.143, H2O.21, H2O.23 MN.17: 4 residues within 4Å: Chain F: H.38, H.167, E.171 Chain V: H.65 6 PLIP interactions: 1 interactions with chain V, 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: V:H.65, F:H.38, F:H.167, F:E.171, H2O.21, H2O.23 MN.18: 5 residues within 4Å: Chain C: R.159 Chain F: R.159 Chain I: R.159 Ligands: MN.9, MN.27 No protein-ligand interaction detected (PLIP) MN.19: 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.25, H2O.26 MN.20: 3 residues within 4Å: Chain G: H.38, H.167, E.171 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.38, G:H.167, G:E.171, H2O.24, H2O.27 MN.21: 5 residues within 4Å: Chain A: R.159 Chain G: R.159 Chain J: R.159 Ligands: MN.3, MN.30 No protein-ligand interaction detected (PLIP) MN.22: 3 residues within 4Å: Chain H: H.64, E.68, H.143 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.64, H:E.68, H:H.143, H2O.28, H2O.30 MN.23: 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.28, H2O.30 MN.24: 5 residues within 4Å: Chain D: R.159 Chain H: R.159 Chain L: R.159 Ligands: MN.12, MN.36 No protein-ligand interaction detected (PLIP) MN.25: 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.32, H2O.34 MN.26: 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.32, H2O.34 MN.27: 5 residues within 4Å: Chain C: R.159 Chain F: R.159 Chain I: R.159 Ligands: MN.9, MN.18 No protein-ligand interaction detected (PLIP) MN.28: 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.36, H2O.38 MN.29: 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.36, H2O.38 MN.30: 5 residues within 4Å: Chain A: R.159 Chain G: R.159 Chain J: R.159 Ligands: MN.3, MN.21 No protein-ligand interaction detected (PLIP) MN.31: 4 residues within 4Å: Chain K: H.64, E.68, H.143 Chain T: H.168 6 PLIP interactions: 3 interactions with chain K, 1 interactions with chain T, 2 Ligand-Water interactions Metal complexes: K:H.64, K:E.68, K:H.143, T:H.168, H2O.40, H2O.42 MN.32: 4 residues within 4Å: Chain K: H.38, H.167, E.171 Chain S: H.65 6 PLIP interactions: 3 interactions with chain K, 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: K:H.38, K:H.167, K:E.171, S:H.65, H2O.40, H2O.42 MN.33: 5 residues within 4Å: Chain B: R.159 Chain E: R.159 Chain K: R.159 Ligands: MN.6, MN.15 No protein-ligand interaction detected (PLIP) MN.34: 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.44, H2O.45 MN.35: 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.43, H2O.46 MN.36: 5 residues within 4Å: Chain D: R.159 Chain H: R.159 Chain L: R.159 Ligands: MN.12, MN.24 No protein-ligand interaction detected (PLIP) MN.37: 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.47, H2O.49 MN.38: 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.47, H2O.49 MN.39: 5 residues within 4Å: Chain M: R.159 Chain S: R.159 Chain V: R.159 Ligands: MN.57, MN.66 No protein-ligand interaction detected (PLIP) MN.40: 4 residues within 4Å: Chain C: H.168 Chain N: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain N, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: N:H.64, N:E.68, N:H.143, C:H.168, H2O.51, H2O.53 MN.41: 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.51, H2O.53 MN.42: 5 residues within 4Å: Chain N: R.159 Chain Q: R.159 Chain W: R.159 Ligands: MN.51, MN.69 No protein-ligand interaction detected (PLIP) MN.43: 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.55, H2O.57 MN.44: 4 residues within 4Å: Chain B: H.65 Chain O: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain O, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: O:H.38, O:H.167, O:E.171, B:H.65, H2O.55, H2O.57 MN.45: 5 residues within 4Å: Chain O: R.159 Chain R: R.159 Chain U: R.159 Ligands: MN.54, MN.63 No protein-ligand interaction detected (PLIP) MN.46: 4 residues within 4Å: Chain B: H.168 Chain P: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain P, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: P:H.64, P:E.68, P:H.143, B:H.168, H2O.59, H2O.61 MN.47: 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.59, H2O.61 MN.48: 3 residues within 4Å: Chain P: R.159 Chain T: R.159 Ligands: MN.60 No protein-ligand interaction detected (PLIP) MN.49: 4 residues within 4Å: Chain J: H.168 Chain Q: H.64, E.68, H.143 6 PLIP interactions: 1 interactions with chain J, 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: J:H.168, Q:H.64, Q:E.68, Q:H.143, H2O.63, H2O.64 MN.50: 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.65 MN.51: 5 residues within 4Å: Chain N: R.159 Chain Q: R.159 Chain W: R.159 Ligands: MN.42, MN.69 No protein-ligand interaction detected (PLIP) MN.52: 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.66, H2O.68 MN.53: 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.66, H2O.68 MN.54: 5 residues within 4Å: Chain O: R.159 Chain R: R.159 Chain U: R.159 Ligands: MN.45, MN.63 No protein-ligand interaction detected (PLIP) MN.55: 4 residues within 4Å: Chain K: H.168 Chain S: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain S, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: S:H.64, S:E.68, S:H.143, K:H.168, H2O.70, H2O.72 MN.56: 4 residues within 4Å: Chain L: H.65 Chain S: H.38, H.167, E.171 6 PLIP interactions: 1 interactions with chain L, 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: L:H.65, S:H.38, S:H.167, S:E.171, H2O.70, H2O.72 MN.57: 5 residues within 4Å: Chain M: R.159 Chain S: R.159 Chain V: R.159 Ligands: MN.39, MN.66 No protein-ligand interaction detected (PLIP) MN.58: 4 residues within 4Å: Chain L: H.168 Chain T: H.64, E.68, H.143 6 PLIP interactions: 3 interactions with chain T, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: T:H.64, T:E.68, T:H.143, L:H.168, H2O.74, H2O.76 MN.59: 4 residues within 4Å: Chain K: H.65 Chain T: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain T, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: T:H.38, T:H.167, T:E.171, K:H.65, H2O.74, H2O.76 MN.60: 3 residues within 4Å: Chain P: R.159 Chain T: R.159 Ligands: MN.48 No protein-ligand interaction detected (PLIP) MN.61: 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.78, H2O.80 MN.62: 4 residues within 4Å: Chain F: H.65 Chain U: H.38, H.167, E.171 6 PLIP interactions: 3 interactions with chain U, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: U:H.38, U:H.167, U:E.171, F:H.65, H2O.78, H2O.80 MN.63: 5 residues within 4Å: Chain O: R.159 Chain R: R.159 Chain U: R.159 Ligands: MN.45, MN.54 No protein-ligand interaction detected (PLIP) MN.64: 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.82, H2O.84 MN.65: 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.82, H2O.84 MN.66: 5 residues within 4Å: Chain M: R.159 Chain S: R.159 Chain V: R.159 Ligands: MN.39, MN.57 No protein-ligand interaction detected (PLIP) MN.67: 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.85, H2O.87 MN.68: 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.85, H2O.87 MN.69: 5 residues within 4Å: Chain N: R.159 Chain Q: R.159 Chain W: R.159 Ligands: MN.42, MN.51 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Crystal structure of Imidazole Glycerol Phosphate Dehydratase from Mycobacterium tuberculosis at 1.61 A resolution. To Be Published

Release Date

2021-04-14

Peptides

Imidazoleglycerol-phosphate dehydratase: ABCDEFGHIJKLMNOPQRSTUVW

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

Imidazoleglycerol-phosphate dehydratase

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