SMTL ID : 9hg0.1

Crystal structure of M. smegmatis GMP reductase with XMP* intermidiate in complex with NADP+ and IMP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

16 x IMP: INOSINIC ACID(Covalent)(Non-covalent)

IMP.1: 20 residues within 4Å: Chain A: A.51, M.53, N.275, G.300, A.301, C.303, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, E.413, G.414 Ligands: NAP.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.275, A:A.301, A:D.336, A:G.338, A:G.359, A:S.360, A:M.387, A:A.388, A:E.413 Water bridges: A:K.294, A:K.294, A:G.300, A:M.302, A:G.337, A:V.339, A:W.361, A:W.361 Salt bridges: A:R.340 IMP.3: 7 residues within 4Å: Chain A: R.60, V.101, T.102, L.115, K.118 Chain H: F.147, R.149 8 PLIP interactions: 1 interactions with chain H, 7 interactions with chain A Hydrogen bonds: H:R.149, A:T.102, A:T.102, A:T.102 Water bridges: A:R.59, A:R.60 Salt bridges: A:R.60, A:K.118 IMP.4: 20 residues within 4Å: Chain B: A.51, M.53, N.275, G.300, A.301, C.303, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, E.413, G.414 Ligands: NAP.5 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.275, B:A.301, B:D.336, B:G.338, B:G.359, B:S.360, B:M.387, B:A.388, B:E.413 Water bridges: B:K.294, B:K.294, B:G.300, B:M.302, B:G.337, B:V.339, B:R.340, B:W.361 Salt bridges: B:R.340 IMP.6: 7 residues within 4Å: Chain B: R.60, V.101, T.102, L.115, K.118 Chain G: F.147, R.149 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:T.102, B:T.102, B:T.102, G:R.149 Water bridges: B:R.59, B:R.60 Salt bridges: B:R.60, B:K.118 IMP.7: 20 residues within 4Å: Chain C: A.51, M.53, N.275, G.300, A.301, C.303, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, E.413, G.414 Ligands: NAP.8 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:N.275, C:A.301, C:D.336, C:G.338, C:G.359, C:S.360, C:M.387, C:A.388, C:E.413 Water bridges: C:K.294, C:K.294, C:K.294, C:G.300, C:G.337, C:V.339, C:R.340, C:W.361 Salt bridges: C:R.340 IMP.9: 8 residues within 4Å: Chain C: R.60, V.101, T.102, L.115, K.118, P.369 Chain F: F.147, R.149 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.102, C:T.102, C:T.102 Water bridges: C:R.59, C:R.60 Salt bridges: C:R.60, C:K.118 IMP.10: 20 residues within 4Å: Chain D: A.51, M.53, N.275, G.300, A.301, C.303, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, E.413, G.414 Ligands: NAP.11 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:N.275, D:A.301, D:D.336, D:G.338, D:G.359, D:S.360, D:M.387, D:A.388, D:E.413 Water bridges: D:K.294, D:K.294, D:G.300, D:M.302, D:G.337, D:V.339, D:R.340, D:R.340 Salt bridges: D:R.340 IMP.12: 8 residues within 4Å: Chain D: R.60, V.101, T.102, L.115, K.118, P.369 Chain E: F.147, R.149 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.102, D:T.102, D:T.102 Water bridges: D:R.59, D:R.60 Salt bridges: D:R.60, D:K.118 IMP.13: 20 residues within 4Å: Chain E: A.51, M.53, P.299, G.300, A.301, C.303, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, E.413, G.414 Ligands: NAP.14 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:N.275, E:A.301, E:D.336, E:G.338, E:G.359, E:S.360, E:S.360, E:M.387, E:A.388, E:E.413 Water bridges: E:K.294, E:K.294, E:G.300, E:M.302, E:G.337, E:V.339, E:R.340, E:W.361 Salt bridges: E:R.340 IMP.15: 7 residues within 4Å: Chain D: F.147, R.149 Chain E: R.60, V.101, T.102, L.115, K.118 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.102, E:T.102 Salt bridges: E:R.60, E:K.118 IMP.16: 21 residues within 4Å: Chain F: A.51, M.53, N.275, G.300, A.301, M.302, C.303, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, E.413, G.414 Ligands: NAP.17 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:N.275, F:A.301, F:D.336, F:G.338, F:G.359, F:S.360, F:M.387, F:A.388, F:E.413 Water bridges: F:K.294, F:K.294, F:K.294, F:G.300, F:V.339, F:V.339, F:R.340, F:W.361 Salt bridges: F:R.340 IMP.18: 7 residues within 4Å: Chain C: F.147, R.149 Chain F: R.60, V.101, T.102, L.115, K.118 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:T.102, F:T.102 Water bridges: F:R.59, F:R.60 Salt bridges: F:R.60, F:K.118 IMP.19: 20 residues within 4Å: Chain G: A.51, M.53, N.275, G.300, A.301, C.303, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, E.413, G.414 Ligands: NAP.20 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:N.275, G:K.294, G:K.294, G:A.301, G:G.338, G:G.359, G:S.360, G:M.387, G:A.388, G:E.413 Water bridges: G:G.300, G:M.302, G:G.337, G:V.339, G:R.340, G:W.361 Salt bridges: G:R.340 IMP.21: 7 residues within 4Å: Chain B: F.147, R.149 Chain G: R.60, V.101, T.102, L.115, K.118 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:T.102, G:T.102 Water bridges: G:R.59, G:R.60 Salt bridges: G:R.60, G:K.118 IMP.23: 20 residues within 4Å: Chain H: A.51, M.53, N.275, G.300, A.301, C.303, D.336, G.337, G.338, R.340, M.357, I.358, G.359, S.360, G.386, M.387, A.388, E.413, G.414 Ligands: NAP.22 19 PLIP interactions: 19 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:M.387, H:A.388, H:E.413 Water bridges: H:K.294, H:K.294, H:K.294, H:G.300, H:M.302, H:V.339, H:V.339, H:R.340, H:W.361 Salt bridges: H:R.340 IMP.24: 8 residues within 4Å: Chain A: F.147, R.149 Chain H: R.60, V.101, T.102, L.115, K.118, P.369 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:T.102, H:T.102 Salt bridges: H:R.60, H:K.118

8 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 23 residues within 4Å: Chain A: N.52, Q.76, N.225, D.246, T.247, A.248, Q.252, K.254, N.275, G.296, V.297, G.298, C.303, T.305, M.387, A.388 Chain D: A.29, S.30, R.31, S.442, T.445, Y.446 Ligands: IMP.1 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:A.248 Hydrogen bonds: A:N.52, A:Q.76, A:N.225, A:N.225, A:D.246, A:T.247, A:A.248, A:Q.252, A:G.296, A:G.298, D:S.30, D:R.31, D:T.445, D:T.445 Water bridges: A:H.249, A:N.275, A:N.275, A:K.294 Salt bridges: D:R.31 pi-Cation interactions: D:R.31 NAP.5: 24 residues within 4Å: Chain A: A.29, S.30, R.31, S.442, T.445, Y.446 Chain B: N.52, Q.76, N.225, D.246, T.247, A.248, Q.252, K.254, N.275, G.296, V.297, G.298, C.303, T.305, M.387, A.388, R.396 Ligands: IMP.4 26 PLIP interactions: 17 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.248 Hydrogen bonds: B:N.52, B:Q.76, B:N.225, B:N.225, B:D.246, B:T.247, B:A.248, B:Q.252, B:K.254, B:N.275, B:G.296, B:G.298, B:R.396, A:S.30, A:R.31, A:T.445, A:T.445 Water bridges: B:H.249, B:H.249, B:K.294, A:S.30, A:S.442, A:Y.446 Salt bridges: A:R.31 pi-Cation interactions: A:R.31 NAP.8: 23 residues within 4Å: Chain B: A.29, S.30, R.31, S.442, T.445, Y.446 Chain C: Q.76, N.225, D.246, T.247, A.248, Q.252, K.254, N.275, G.296, V.297, G.298, C.303, T.305, M.387, A.388, R.396 Ligands: IMP.7 24 PLIP interactions: 18 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:A.248 Hydrogen bonds: C:Q.76, C:N.225, C:N.225, C:D.246, C:T.247, C:T.247, C:A.248, C:Q.252, C:K.254, C:G.296, C:G.298, C:R.396, B:S.30, B:R.31, B:T.445, B:T.445 Water bridges: C:H.249, C:H.249, C:N.275, C:K.294, C:K.294 Salt bridges: B:R.31 pi-Cation interactions: B:R.31 NAP.11: 23 residues within 4Å: Chain C: A.29, S.30, R.31, S.442, T.445, Y.446 Chain D: Q.76, N.225, D.246, T.247, A.248, Q.252, K.254, N.275, G.296, V.297, G.298, C.303, T.305, M.387, A.388, R.396 Ligands: IMP.10 21 PLIP interactions: 6 interactions with chain C, 15 interactions with chain D Hydrogen bonds: C:S.30, C:R.31, C:T.445, C:T.445, D:N.52, D:Q.76, D:N.225, D:N.225, D:D.246, D:T.247, D:A.248, D:Q.252, D:K.254, D:N.275, D:G.296, D:G.298, D:R.396 Salt bridges: C:R.31 pi-Cation interactions: C:R.31 Hydrophobic interactions: D:A.248 Water bridges: D:K.294 NAP.14: 24 residues within 4Å: Chain E: N.52, Q.76, N.225, D.246, T.247, A.248, Q.252, K.254, N.275, G.296, V.297, G.298, C.303, T.305, M.387, A.388, R.396 Chain H: A.29, S.30, R.31, S.442, T.445, Y.446 Ligands: IMP.13 26 PLIP interactions: 17 interactions with chain E, 9 interactions with chain H Hydrophobic interactions: E:A.248 Hydrogen bonds: E:N.52, E:Q.76, E:N.225, E:N.225, E:D.246, E:T.247, E:A.248, E:Q.252, E:K.254, E:G.296, E:G.298, E:R.396, H:S.30, H:R.31, H:T.445, H:T.445 Water bridges: E:H.249, E:N.275, E:N.275, E:K.294, H:R.31, H:R.31, H:S.442 Salt bridges: H:R.31 pi-Cation interactions: H:R.31 NAP.17: 24 residues within 4Å: Chain E: A.29, S.30, R.31, S.442, T.445, Y.446 Chain F: N.52, Q.76, I.224, N.225, D.246, T.247, A.248, Q.252, N.275, G.296, V.297, G.298, C.303, T.305, M.387, A.388, R.396 Ligands: IMP.16 20 PLIP interactions: 5 interactions with chain E, 15 interactions with chain F Hydrogen bonds: E:S.30, E:R.31, E:T.445, F:N.52, F:Q.76, F:N.225, F:N.225, F:D.246, F:A.248, F:Q.252, F:N.275, F:G.296, F:G.298, F:R.396 Salt bridges: E:R.31 pi-Cation interactions: E:R.31 Hydrophobic interactions: F:A.248 Water bridges: F:H.249, F:K.294, F:K.294 NAP.20: 24 residues within 4Å: Chain F: A.29, S.30, R.31, S.442, T.445, Y.446 Chain G: Q.76, I.224, N.225, D.246, T.247, A.248, Q.252, K.254, N.275, G.296, V.297, G.298, C.303, T.305, M.387, A.388, R.396 Ligands: IMP.19 21 PLIP interactions: 15 interactions with chain G, 6 interactions with chain F Hydrophobic interactions: G:A.248 Hydrogen bonds: G:N.52, G:Q.76, G:N.225, G:N.225, G:D.246, G:A.248, G:Q.252, G:N.275, G:G.296, G:G.298, G:R.396, F:S.30, F:R.31, F:T.445, F:T.445 Water bridges: G:H.249, G:K.294, G:K.294 Salt bridges: F:R.31 pi-Cation interactions: F:R.31 NAP.22: 23 residues within 4Å: Chain G: A.29, S.30, R.31, S.442, T.445, Y.446 Chain H: N.52, Q.76, N.225, D.246, T.247, A.248, Q.252, N.275, G.296, V.297, G.298, C.303, T.305, M.387, A.388, R.396 Ligands: IMP.23 21 PLIP interactions: 15 interactions with chain H, 6 interactions with chain G Hydrophobic interactions: H:A.248 Hydrogen bonds: H:N.52, H:Q.76, H:N.225, H:N.225, H:D.246, H:D.246, H:A.248, H:Q.252, H:N.275, H:G.296, H:G.298, H:R.396, G:S.30, G:R.31, G:T.445, G:T.445 Water bridges: H:K.294, H:K.294 Salt bridges: G:R.31 pi-Cation interactions: G:R.31

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
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

GMP reductase

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