SMTL ID : 9hg1.2 (1 other biounit)

Crystal structure of M. smegmatis GMP reductase in complex with GMP and ATP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 12 residues within 4Å: Chain A: T.54, G.58, R.59, R.60, P.75, L.78, P.79, A.82, K.118, P.369 Chain H: F.147, R.149 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain H Hydrogen bonds: A:T.54, A:R.59, H:R.149 Water bridges: A:A.57 Salt bridges: A:R.59, A:R.59, A:R.60, A:K.118 pi-Cation interactions: H:R.149, H:R.149 ATP.3: 11 residues within 4Å: Chain B: T.54, G.58, R.59, R.60, P.75, L.78, P.79, K.118, P.369 Chain G: F.147, R.149 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain G Hydrogen bonds: B:T.54, B:R.59, G:E.106, G:E.106 Water bridges: B:A.57, B:R.60, B:R.60, B:T.86, G:R.149 Salt bridges: B:R.59, B:R.59, B:R.60, B:K.118 pi-Cation interactions: G:R.149, G:R.149 ATP.5: 13 residues within 4Å: Chain C: T.54, G.58, R.59, R.60, P.75, L.78, P.79, A.82, K.118, P.369 Chain F: E.106, F.147, R.149 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain F Hydrogen bonds: C:T.54, C:R.59, F:E.106, F:E.106, F:R.149 Water bridges: C:A.57, C:R.59, C:R.59, C:R.60, C:R.60, C:T.86 Salt bridges: C:R.59, C:R.59, C:R.60 pi-Cation interactions: F:R.149, F:R.149 ATP.8: 12 residues within 4Å: Chain D: T.54, G.58, R.59, R.60, P.75, L.78, P.79, A.82, K.118, P.369 Chain E: F.147, R.149 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:T.54, D:R.59, E:R.149 Water bridges: D:A.57, D:R.60, D:R.60, D:T.86, D:T.86, E:E.106 Salt bridges: D:R.60, D:K.118 pi-Cation interactions: E:R.149, E:R.149 ATP.10: 11 residues within 4Å: Chain D: F.147, R.149 Chain E: T.54, G.58, R.59, R.60, P.75, L.78, P.79, K.118, P.369 12 PLIP interactions: 4 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:R.149, E:T.54, E:R.59 Water bridges: D:R.149, E:K.118, E:K.118 pi-Cation interactions: D:R.149, D:R.149 Salt bridges: E:R.59, E:R.59, E:R.60, E:K.118 ATP.12: 12 residues within 4Å: Chain C: E.106, F.147, R.149 Chain F: T.54, G.58, R.59, R.60, P.75, L.78, P.79, K.118, P.369 10 PLIP interactions: 6 interactions with chain F, 4 interactions with chain C Hydrogen bonds: F:T.54, F:R.59, C:E.106, C:R.149 Water bridges: F:A.57 Salt bridges: F:R.59, F:R.59, F:R.60 pi-Cation interactions: C:R.149, C:R.149 ATP.14: 13 residues within 4Å: Chain B: E.106, F.147, R.149 Chain G: T.54, G.58, R.59, R.60, P.75, L.78, P.79, T.86, K.118, P.369 10 PLIP interactions: 7 interactions with chain G, 3 interactions with chain B Hydrogen bonds: G:T.54, G:R.59, G:R.59, B:E.106 Water bridges: G:A.57 Salt bridges: G:R.59, G:R.60, G:K.118 pi-Cation interactions: B:R.149, B:R.149 ATP.16: 12 residues within 4Å: Chain A: F.147, R.149 Chain H: T.54, G.58, R.59, R.60, P.75, L.78, P.79, A.82, K.118, P.369 14 PLIP interactions: 10 interactions with chain H, 4 interactions with chain A Hydrogen bonds: H:T.54, H:R.59, A:R.149 Water bridges: H:A.57, H:R.60, H:R.60, H:K.118, A:R.149, A:R.149 Salt bridges: H:R.59, H:R.59, H:R.60, H:K.118 pi-Cation interactions: A:R.149

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

5GP.2: 20 residues within 4Å: Chain A: A.51, M.53, N.275, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.275, A:A.301, A:T.305, A:T.305, A:D.336, A:G.338, A:G.359, A:S.360, A:S.360, A:M.387, A:A.388, A:R.391 Water bridges: A:K.294, A:V.339, A:V.339, A:V.339, A:W.361 Salt bridges: A:E.413 5GP.4: 21 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, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.275, B:A.301, B:T.305, B:T.305, B:D.336, B:G.338, B:G.359, B:S.360, B:S.360, B:M.387, B:A.388, B:R.391 Water bridges: B:K.294, B:K.294, B:M.302, B:G.337, B:V.339, B:W.361, B:G.386 Salt bridges: B:E.413 5GP.6: 20 residues within 4Å: Chain C: A.51, M.53, N.275, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:N.275, C:K.294, C:K.294, C:A.301, C:T.305, C:T.305, C:G.338, C:G.359, C:S.360, C:S.360, C:M.387, C:A.388, C:R.391 Water bridges: C:G.337, C:V.339, C:V.339, C:W.361 Salt bridges: C:E.413 5GP.7: 20 residues within 4Å: Chain D: A.51, M.53, N.275, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:N.275, D:A.301, D:T.305, D:T.305, D:D.336, D:G.338, D:G.359, D:S.360, D:S.360, D:M.387, D:A.388, D:R.391 Water bridges: D:K.294, D:K.294, D:M.302, D:G.337, D:V.339, D:V.339, D:S.360, D:S.360, D:W.361 Salt bridges: D:E.413 5GP.9: 19 residues within 4Å: Chain E: A.51, M.53, N.275, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, M.357, G.359, S.360, G.386, M.387, A.388, R.391, E.413 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:N.275, E:A.301, E:T.305, E:D.336, E:G.338, E:G.359, E:S.360, E:S.360, E:S.360, E:M.387, E:A.388, E:R.391 Water bridges: E:K.294, E:G.337, E:V.339, E:W.361 Salt bridges: E:E.413 5GP.11: 20 residues within 4Å: Chain F: A.51, M.53, N.275, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:N.275, F:A.301, F:T.305, F:D.336, F:G.338, F:G.359, F:S.360, F:S.360, F:M.387, F:A.388, F:R.391 Water bridges: F:W.361, F:R.391, F:R.391 Salt bridges: F:E.413 5GP.13: 20 residues within 4Å: Chain G: A.51, M.53, N.275, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 21 PLIP interactions: 21 interactions with chain G Hydrogen bonds: G:N.275, G:A.301, G:T.305, G:D.336, G:G.338, G:G.359, G:S.360, G:S.360, G:M.387, G:A.388, G:R.391 Water bridges: G:K.294, G:K.294, G:M.302, G:G.337, G:V.339, G:V.339, G:V.339, G:W.361, G:S.416 Salt bridges: G:E.413 5GP.15: 20 residues within 4Å: Chain H: A.51, M.53, N.275, G.300, A.301, M.302, C.303, T.305, D.336, G.337, G.338, M.357, I.358, G.359, S.360, G.386, M.387, A.388, R.391, E.413 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:N.275, H:A.301, H:D.336, H:G.338, H:G.359, H:S.360, H:S.360, H:M.387, H:A.388, H:R.391 Water bridges: H:K.294, H:K.294, H:M.302, H:G.337, H:V.339, H:W.361 Salt bridges: H:E.413

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

2025-08-27

Peptides

GMP reductase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

GMP reductase

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