SMTL ID : 8ry3.1

CryoEM structure of M. smegmatis GMP reductase in complex with GMP and GTP at pH 6.6, extended conformation I.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 22 residues within 4Å: Chain A: A.51, M.53, N.275, P.299, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.275, A:K.294, A:A.301, A:T.305, A:G.338, A:G.359, A:S.360, A:S.360, A:M.387, A:A.388, A:R.391 Salt bridges: A:R.340, A:E.413 5GP.3: 22 residues within 4Å: Chain B: A.51, M.53, N.275, P.299, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.275, B:K.294, B:A.301, B:T.305, B:G.338, B:G.359, B:S.360, B:S.360, B:M.387, B:A.388, B:R.391 Salt bridges: B:R.340, B:E.413 5GP.5: 22 residues within 4Å: Chain C: A.51, M.53, N.275, P.299, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:N.275, C:K.294, C:A.301, C:T.305, C:G.338, C:G.359, C:S.360, C:S.360, C:M.387, C:A.388, C:R.391 Salt bridges: C:R.340, C:E.413 5GP.7: 22 residues within 4Å: Chain D: A.51, M.53, N.275, P.299, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:N.275, D:K.294, D:A.301, D:T.305, D:G.338, D:G.359, D:S.360, D:S.360, D:M.387, D:A.388, D:R.391 Salt bridges: D:R.340, D:E.413 5GP.9: 22 residues within 4Å: Chain E: A.51, M.53, N.275, P.299, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:N.275, E:K.294, E:A.301, E:T.305, E:T.305, E:G.338, E:G.359, E:S.360, E:S.360, E:M.387, E:A.388, E:R.391 Salt bridges: E:R.340, E:E.413 5GP.11: 22 residues within 4Å: Chain F: A.51, M.53, N.275, P.299, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:N.275, F:K.294, F:A.301, F:T.305, F:T.305, F:G.338, F:G.359, F:S.360, F:S.360, F:M.387, F:A.388, F:R.391 Salt bridges: F:R.340, F:E.413 5GP.13: 22 residues within 4Å: Chain G: A.51, M.53, N.275, P.299, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:N.275, G:K.294, G:A.301, G:T.305, G:T.305, G:G.338, G:G.359, G:S.360, G:S.360, G:M.387, G:A.388, G:R.391 Salt bridges: G:R.340, G:E.413 5GP.15: 22 residues within 4Å: Chain H: A.51, M.53, N.275, P.299, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:N.275, H:K.294, H:A.301, H:T.305, H:T.305, H:G.338, H:G.359, H:S.360, H:S.360, H:M.387, H:A.388, H:R.391 Salt bridges: H:R.340, H:E.413

8 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 12 residues within 4Å: Chain A: G.58, R.59, R.60, P.100, V.101, T.102, L.115, K.118, P.369 Chain H: D.145, F.147, R.149 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.59, A:R.59, A:R.60, A:T.102, A:T.102, A:T.102, A:P.369 Salt bridges: A:R.59, A:R.59, A:R.60, A:R.60, A:R.60, A:K.118, A:K.118 GTP.4: 12 residues within 4Å: Chain B: G.58, R.59, R.60, P.100, V.101, T.102, L.115, K.118, P.369 Chain G: D.145, F.147, R.149 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.59, B:R.59, B:R.60, B:T.102, B:T.102, B:T.102, B:P.369 Salt bridges: B:R.59, B:R.59, B:R.60, B:R.60, B:R.60, B:K.118, B:K.118 GTP.6: 12 residues within 4Å: Chain C: G.58, R.59, R.60, P.100, V.101, T.102, L.115, K.118, P.369 Chain F: D.145, F.147, R.149 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:R.59, C:R.59, C:R.60, C:T.102, C:T.102, C:T.102, C:P.369 Salt bridges: C:R.59, C:R.59, C:R.60, C:R.60, C:R.60, C:K.118, C:K.118 GTP.8: 12 residues within 4Å: Chain D: G.58, R.59, R.60, P.100, V.101, T.102, L.115, K.118, P.369 Chain E: D.145, F.147, R.149 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:R.59, D:R.59, D:R.60, D:T.102, D:T.102, D:T.102, D:P.369 Salt bridges: D:R.59, D:R.59, D:R.60, D:R.60, D:R.60, D:K.118, D:K.118 GTP.10: 12 residues within 4Å: Chain D: D.145, F.147, R.149 Chain E: G.58, R.59, R.60, P.100, V.101, T.102, L.115, K.118, P.369 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:R.59, E:R.59, E:R.60, E:T.102, E:T.102, E:T.102, E:T.102, E:P.369 Salt bridges: E:R.59, E:R.59, E:R.60, E:R.60, E:R.60, E:K.118, E:K.118 GTP.12: 12 residues within 4Å: Chain C: D.145, F.147, R.149 Chain F: G.58, R.59, R.60, P.100, V.101, T.102, L.115, K.118, P.369 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:R.59, F:R.59, F:R.60, F:T.102, F:T.102, F:T.102, F:T.102, F:P.369 Salt bridges: F:R.59, F:R.59, F:R.60, F:R.60, F:R.60, F:K.118, F:K.118 GTP.14: 12 residues within 4Å: Chain B: D.145, F.147, R.149 Chain G: G.58, R.59, R.60, P.100, V.101, T.102, L.115, K.118, P.369 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:R.59, G:R.59, G:R.60, G:T.102, G:T.102, G:T.102, G:T.102, G:P.369 Salt bridges: G:R.59, G:R.59, G:R.60, G:R.60, G:R.60, G:K.118, G:K.118 GTP.16: 12 residues within 4Å: Chain A: D.145, F.147, R.149 Chain H: G.58, R.59, R.60, P.100, V.101, T.102, L.115, K.118, P.369 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:R.59, H:R.59, H:R.60, H:T.102, H:T.102, H:T.102, H:T.102, H:P.369 Salt bridges: H:R.59, H:R.59, H:R.60, H:R.60, H:R.60, H:K.118, H:K.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dolezal, M. et al., Structural basis for allosteric regulation of mycobacterial guanosine 5'-monophosphate reductase with ATP and GTP. To Be Published

Release Date

2025-08-20

Peptides

GMP reductase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

GMP reductase

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