SMTL ID : 9m2p.1

Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, apo structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 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: D.114, H.183 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.79, A:E.83, A:H.158, D:H.183, H2O.1 MN.2: 4 residues within 4Å: Chain A: H.53, H.182, E.186 Chain B: H.80 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.53, A:H.182, A:E.186, B:H.80, H2O.1 MN.3: 5 residues within 4Å: Chain A: D.114, H.183 Chain B: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.79, B:E.83, B:H.158, A:H.183, H2O.1 MN.4: 4 residues within 4Å: Chain B: H.53, H.182, E.186 Chain C: H.80 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.53, B:H.182, B:E.186, C:H.80, H2O.1 MN.5: 5 residues within 4Å: Chain B: D.114, H.183 Chain C: H.79, E.83, H.158 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.183, C:H.79, C:E.83, C:H.158, H2O.1 MN.6: 4 residues within 4Å: Chain C: H.53, H.182, E.186 Chain D: H.80 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:H.53, C:H.182, C:E.186, D:H.80, H2O.1 MN.7: 5 residues within 4Å: Chain C: D.114, H.183 Chain D: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.79, D:E.83, D:H.158, C:H.183, H2O.1 MN.8: 4 residues within 4Å: Chain A: H.80 Chain D: H.53, H.182, E.186 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:H.53, D:H.182, D:E.186, A:H.80, H2O.1 MN.9: 5 residues within 4Å: Chain E: H.79, E.83, H.158 Chain O: D.114, H.183 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: E:H.79, E:E.83, E:H.158, O:H.183, H2O.1 MN.10: 4 residues within 4Å: Chain E: H.53, H.182, E.186 Chain J: H.80 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: E:H.53, E:H.182, E:E.186, J:H.80, H2O.1 MN.11: 5 residues within 4Å: Chain F: H.79, E.83, H.158 Chain L: D.114, H.183 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: F:H.79, F:E.83, F:H.158, L:H.183, H2O.1 MN.12: 4 residues within 4Å: Chain F: H.53, H.182, E.186 Chain M: H.80 5 PLIP interactions: 1 interactions with chain M, 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: M:H.80, F:H.53, F:H.182, F:E.186, H2O.1 MN.13: 5 residues within 4Å: Chain G: H.79, E.83, H.158 Chain I: D.114, H.183 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: G:H.79, G:E.83, G:H.158, I:H.183, H2O.1 MN.14: 4 residues within 4Å: Chain G: H.53, H.182, E.186 Chain P: H.80 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: G:H.53, G:H.182, G:E.186, P:H.80, H2O.1 MN.15: 5 residues within 4Å: Chain H: H.79, E.83, H.158 Chain W: D.114, H.183 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: H:H.79, H:E.83, H:H.158, W:H.183, H2O.1 MN.16: 4 residues within 4Å: Chain H: H.53, H.182, E.186 Chain U: H.80 5 PLIP interactions: 1 interactions with chain U, 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: U:H.80, H:H.53, H:H.182, H:E.186, H2O.1 MN.17: 5 residues within 4Å: Chain I: H.79, E.83, H.158 Chain R: D.114, H.183 5 PLIP interactions: 1 interactions with chain R, 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: R:H.183, I:H.79, I:E.83, I:H.158, H2O.1 MN.18: 4 residues within 4Å: Chain G: H.80 Chain I: H.53, H.182, E.186 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: I:H.53, I:H.182, I:E.186, G:H.80, H2O.1 MN.19: 5 residues within 4Å: Chain E: D.114, H.183 Chain J: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: J:H.79, J:E.83, J:H.158, E:H.183, H2O.1 MN.20: 4 residues within 4Å: Chain J: H.53, H.182, E.186 Chain S: H.80 5 PLIP interactions: 1 interactions with chain S, 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: S:H.80, J:H.53, J:H.182, J:E.186, H2O.1 MN.21: 5 residues within 4Å: Chain K: H.79, E.83, H.158 Chain U: D.114, H.183 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain U, 1 Ligand-Water interactions Metal complexes: K:H.79, K:E.83, K:H.158, U:H.183, H2O.1 MN.22: 4 residues within 4Å: Chain K: H.53, H.182, E.186 Chain W: H.80 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: K:H.53, K:H.182, K:E.186, W:H.80, H2O.1 MN.23: 5 residues within 4Å: Chain L: H.79, E.83, H.158 Chain T: D.114, H.183 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain T, 1 Ligand-Water interactions Metal complexes: L:H.79, L:E.83, L:H.158, T:H.183, H2O.1 MN.24: 4 residues within 4Å: Chain F: H.80 Chain L: H.53, H.182, E.186 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: L:H.53, L:H.182, L:E.186, F:H.80, H2O.1 MN.25: 5 residues within 4Å: Chain F: D.114, H.183 Chain M: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain M, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: M:H.79, M:E.83, M:H.158, F:H.183, H2O.1 MN.26: 4 residues within 4Å: Chain M: H.53, H.182, E.186 Chain T: H.80 5 PLIP interactions: 3 interactions with chain M, 1 interactions with chain T, 1 Ligand-Water interactions Metal complexes: M:H.53, M:H.182, M:E.186, T:H.80, H2O.1 MN.27: 5 residues within 4Å: Chain N: H.79, E.83, H.158 Chain V: D.114, H.183 5 PLIP interactions: 3 interactions with chain N, 1 interactions with chain V, 1 Ligand-Water interactions Metal complexes: N:H.79, N:E.83, N:H.158, V:H.183, H2O.2 MN.28: 4 residues within 4Å: Chain N: H.53, H.182, E.186 Chain X: H.80 5 PLIP interactions: 1 interactions with chain X, 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: X:H.80, N:H.53, N:H.182, N:E.186, H2O.2 MN.29: 5 residues within 4Å: Chain O: H.79, E.83, H.158 Chain S: D.114, H.183 5 PLIP interactions: 3 interactions with chain O, 1 interactions with chain S, 1 Ligand-Water interactions Metal complexes: O:H.79, O:E.83, O:H.158, S:H.183, H2O.2 MN.30: 4 residues within 4Å: Chain E: H.80 Chain O: H.53, H.182, E.186 5 PLIP interactions: 3 interactions with chain O, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: O:H.53, O:H.182, O:E.186, E:H.80, H2O.2 MN.31: 5 residues within 4Å: Chain G: D.114, H.183 Chain P: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain P, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: P:H.79, P:E.83, P:H.158, G:H.183, H2O.2 MN.32: 4 residues within 4Å: Chain P: H.53, H.182, E.186 Chain R: H.80 5 PLIP interactions: 1 interactions with chain R, 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: R:H.80, P:H.53, P:H.182, P:E.186, H2O.2 MN.33: 5 residues within 4Å: Chain Q: H.79, E.83, H.158 Chain X: D.114, H.183 5 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain X, 1 Ligand-Water interactions Metal complexes: Q:H.79, Q:E.83, Q:H.158, X:H.183, H2O.2 MN.34: 4 residues within 4Å: Chain Q: H.53, H.182, E.186 Chain V: H.80 5 PLIP interactions: 1 interactions with chain V, 3 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: V:H.80, Q:H.53, Q:H.182, Q:E.186, H2O.2 MN.35: 5 residues within 4Å: Chain P: D.114, H.183 Chain R: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain R, 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: R:H.79, R:E.83, R:H.158, P:H.183, H2O.2 MN.36: 4 residues within 4Å: Chain I: H.80 Chain R: H.53, H.182, E.186 5 PLIP interactions: 3 interactions with chain R, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: R:H.53, R:H.182, R:E.186, I:H.80, H2O.2 MN.37: 5 residues within 4Å: Chain J: D.114, H.183 Chain S: H.79, E.83, H.158 5 PLIP interactions: 1 interactions with chain J, 3 interactions with chain S, 1 Ligand-Water interactions Metal complexes: J:H.183, S:H.79, S:E.83, S:H.158, H2O.2 MN.38: 4 residues within 4Å: Chain O: H.80 Chain S: H.53, H.182, E.186 5 PLIP interactions: 3 interactions with chain S, 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: S:H.53, S:H.182, S:E.186, O:H.80, H2O.2 MN.39: 5 residues within 4Å: Chain M: D.114, H.183 Chain T: H.79, E.83, H.158 5 PLIP interactions: 1 interactions with chain M, 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: M:H.183, T:H.79, T:E.83, T:H.158, H2O.2 MN.40: 4 residues within 4Å: Chain L: H.80 Chain T: H.53, H.182, E.186 5 PLIP interactions: 1 interactions with chain L, 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: L:H.80, T:H.53, T:H.182, T:E.186, H2O.2 MN.41: 5 residues within 4Å: Chain H: D.114, H.183 Chain U: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain U, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: U:H.79, U:E.83, U:H.158, H:H.183, H2O.2 MN.42: 4 residues within 4Å: Chain K: H.80 Chain U: H.53, H.182, E.186 5 PLIP interactions: 1 interactions with chain K, 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: K:H.80, U:H.53, U:H.182, U:E.186, H2O.2 MN.43: 5 residues within 4Å: Chain Q: D.114, H.183 Chain V: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain V, 1 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: V:H.79, V:E.83, V:H.158, Q:H.183, H2O.2 MN.44: 4 residues within 4Å: Chain N: H.80 Chain V: H.53, H.182, E.186 5 PLIP interactions: 1 interactions with chain N, 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: N:H.80, V:H.53, V:H.182, V:E.186, H2O.2 MN.45: 5 residues within 4Å: Chain K: D.114, H.183 Chain W: H.79, E.83, H.158 5 PLIP interactions: 3 interactions with chain W, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: W:H.79, W:E.83, W:H.158, K:H.183, H2O.2 MN.46: 4 residues within 4Å: Chain H: H.80 Chain W: H.53, H.182, E.186 5 PLIP interactions: 3 interactions with chain W, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: W:H.53, W:H.182, W:E.186, H:H.80, H2O.2 MN.47: 5 residues within 4Å: Chain N: D.114, H.183 Chain X: H.79, E.83, H.158 5 PLIP interactions: 1 interactions with chain N, 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: N:H.183, X:H.79, X:E.83, X:H.158, H2O.2 MN.48: 4 residues within 4Å: Chain Q: H.80 Chain X: H.53, H.182, E.186 5 PLIP interactions: 3 interactions with chain X, 1 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: X:H.53, X:H.182, X:E.186, Q:H.80, H2O.2

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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