SMTL ID : 6jig.1

Crystal structure of GMP reductase C318A from Trypanosoma brucei in complex with guanosine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

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

5GP.1: 20 residues within 4Å: Chain A: S.52, M.54, N.290, G.315, S.316, I.317, A.318, T.320, D.351, G.352, G.353, M.372, L.373, G.374, N.375, G.400, M.401, A.402, E.428, G.429 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.52, A:N.290, A:T.320, A:D.351, A:G.353, A:G.374, A:N.375, A:M.401, A:A.402, A:G.403, A:E.428 Water bridges: A:K.309, A:K.309, A:G.313, A:G.313, A:T.320, A:T.320, A:L.354, A:L.354, A:L.354, A:L.354 5GP.2: 16 residues within 4Å: Chain A: R.93, A.94, Q.95, S.96, I.99, P.102, R.103, R.123, V.127, G.128, C.129, L.206, T.208, S.210, D.211, K.214 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.93, A:S.96, A:R.103, A:R.123, A:G.128, A:C.129, A:C.129, A:C.129, A:S.210, A:D.211, A:K.214 5GP.4: 20 residues within 4Å: Chain B: S.52, M.54, N.290, G.315, S.316, I.317, A.318, T.320, D.351, G.352, G.353, M.372, L.373, G.374, N.375, G.400, M.401, A.402, E.428, G.429 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:S.52, B:N.290, B:T.320, B:D.351, B:G.353, B:G.374, B:N.375, B:M.401, B:A.402, B:G.403, B:E.428 Water bridges: B:K.309, B:K.309, B:G.313, B:G.313, B:T.320, B:T.320, B:L.354, B:L.354, B:L.354, B:L.354 5GP.5: 16 residues within 4Å: Chain B: R.93, A.94, Q.95, S.96, I.99, P.102, R.103, R.123, V.127, G.128, C.129, L.206, T.208, S.210, D.211, K.214 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.93, B:S.96, B:R.103, B:R.123, B:G.128, B:C.129, B:C.129, B:C.129, B:S.210, B:D.211, B:K.214 5GP.7: 20 residues within 4Å: Chain C: S.52, M.54, N.290, G.315, S.316, I.317, A.318, T.320, D.351, G.352, G.353, M.372, L.373, G.374, N.375, G.400, M.401, A.402, E.428, G.429 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:S.52, C:N.290, C:T.320, C:D.351, C:G.353, C:G.374, C:N.375, C:M.401, C:A.402, C:G.403, C:E.428 Water bridges: C:K.309, C:K.309, C:G.313, C:G.313, C:T.320, C:T.320, C:L.354, C:L.354, C:L.354, C:L.354 5GP.8: 16 residues within 4Å: Chain C: R.93, A.94, Q.95, S.96, I.99, P.102, R.103, R.123, V.127, G.128, C.129, L.206, T.208, S.210, D.211, K.214 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.93, C:S.96, C:R.103, C:R.123, C:G.128, C:C.129, C:C.129, C:C.129, C:S.210, C:D.211, C:K.214 5GP.10: 20 residues within 4Å: Chain D: S.52, M.54, N.290, G.315, S.316, I.317, A.318, T.320, D.351, G.352, G.353, M.372, L.373, G.374, N.375, G.400, M.401, A.402, E.428, G.429 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:S.52, D:N.290, D:T.320, D:D.351, D:G.353, D:G.374, D:N.375, D:M.401, D:A.402, D:G.403, D:E.428 Water bridges: D:K.309, D:K.309, D:G.313, D:G.313, D:T.320, D:T.320, D:L.354, D:L.354, D:L.354, D:L.354 5GP.11: 16 residues within 4Å: Chain D: R.93, A.94, Q.95, S.96, I.99, P.102, R.103, R.123, V.127, G.128, C.129, L.206, T.208, S.210, D.211, K.214 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:R.93, D:S.96, D:R.103, D:R.123, D:G.128, D:C.129, D:C.129, D:C.129, D:S.210, D:D.211, D:K.214 5GP.13: 20 residues within 4Å: Chain E: S.52, M.54, N.290, G.315, S.316, I.317, A.318, T.320, D.351, G.352, G.353, M.372, L.373, G.374, N.375, G.400, M.401, A.402, E.428, G.429 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:S.52, E:N.290, E:T.320, E:T.320, E:D.351, E:G.353, E:G.374, E:N.375, E:M.401, E:A.402, E:G.403, E:E.428 Water bridges: E:K.309, E:K.309, E:G.313, E:G.313, E:L.354, E:L.354, E:L.354, E:L.354 5GP.14: 16 residues within 4Å: Chain E: R.93, A.94, Q.95, S.96, I.99, P.102, R.103, R.123, V.127, G.128, C.129, L.206, T.208, S.210, D.211, K.214 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:R.93, E:S.96, E:R.103, E:R.123, E:G.128, E:C.129, E:C.129, E:C.129, E:S.210, E:D.211, E:K.214 5GP.16: 20 residues within 4Å: Chain F: S.52, M.54, N.290, G.315, S.316, I.317, A.318, T.320, D.351, G.352, G.353, M.372, L.373, G.374, N.375, G.400, M.401, A.402, E.428, G.429 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:S.52, F:N.290, F:T.320, F:T.320, F:D.351, F:G.353, F:G.374, F:N.375, F:M.401, F:A.402, F:G.403, F:E.428 Water bridges: F:K.309, F:K.309, F:G.313, F:G.313, F:L.354, F:L.354, F:L.354, F:L.354 5GP.17: 16 residues within 4Å: Chain F: R.93, A.94, Q.95, S.96, I.99, P.102, R.103, R.123, V.127, G.128, C.129, L.206, T.208, S.210, D.211, K.214 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:R.93, F:S.96, F:R.103, F:R.123, F:G.128, F:C.129, F:C.129, F:C.129, F:S.210, F:D.211, F:K.214 5GP.19: 20 residues within 4Å: Chain G: S.52, M.54, N.290, G.315, S.316, I.317, A.318, T.320, D.351, G.352, G.353, M.372, L.373, G.374, N.375, G.400, M.401, A.402, E.428, G.429 20 PLIP interactions: 20 interactions with chain G Hydrogen bonds: G:S.52, G:N.290, G:T.320, G:T.320, G:D.351, G:G.353, G:G.374, G:N.375, G:M.401, G:A.402, G:G.403, G:E.428 Water bridges: G:K.309, G:K.309, G:G.313, G:G.313, G:L.354, G:L.354, G:L.354, G:L.354 5GP.20: 16 residues within 4Å: Chain G: R.93, A.94, Q.95, S.96, I.99, P.102, R.103, R.123, V.127, G.128, C.129, L.206, T.208, S.210, D.211, K.214 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:R.93, G:S.96, G:R.103, G:R.123, G:G.128, G:C.129, G:C.129, G:C.129, G:S.210, G:D.211, G:K.214 5GP.22: 20 residues within 4Å: Chain H: S.52, M.54, N.290, G.315, S.316, I.317, A.318, T.320, D.351, G.352, G.353, M.372, L.373, G.374, N.375, G.400, M.401, A.402, E.428, G.429 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:S.52, H:N.290, H:T.320, H:T.320, H:D.351, H:G.353, H:G.374, H:N.375, H:M.401, H:A.402, H:G.403, H:E.428 Water bridges: H:K.309, H:K.309, H:G.313, H:G.313, H:L.354, H:L.354, H:L.354, H:L.354 5GP.23: 16 residues within 4Å: Chain H: R.93, A.94, Q.95, S.96, I.99, P.102, R.103, R.123, V.127, G.128, C.129, L.206, T.208, S.210, D.211, K.214 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:R.93, H:S.96, H:R.103, H:R.123, H:G.128, H:C.129, H:C.129, H:C.129, H:S.210, H:D.211, H:K.214

8 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: G.313, P.314, G.315, A.318 Chain C: E.482, S.483, G.484, H.486 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:G.313, A:G.315, A:A.318, C:E.482, C:G.484 K.6: 8 residues within 4Å: Chain B: G.313, P.314, G.315, A.318 Chain D: E.482, S.483, G.484, H.486 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:G.313, B:G.315, B:A.318, D:E.482, D:G.484 K.9: 8 residues within 4Å: Chain B: E.482, S.483, G.484, H.486 Chain C: G.313, P.314, G.315, A.318 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:E.482, B:G.484, C:G.313, C:G.315, C:A.318 K.12: 8 residues within 4Å: Chain A: E.482, S.483, G.484, H.486 Chain D: G.313, P.314, G.315, A.318 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Metal complexes: A:E.482, A:G.484, D:G.313, D:G.315, D:A.318 K.15: 8 residues within 4Å: Chain E: G.313, P.314, G.315, A.318 Chain G: E.482, S.483, G.484, H.486 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain E Metal complexes: G:E.482, G:G.484, E:G.313, E:G.315, E:A.318 K.18: 8 residues within 4Å: Chain F: G.313, P.314, G.315, A.318 Chain H: E.482, S.483, G.484, H.486 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain H Metal complexes: F:G.313, F:G.315, F:A.318, H:E.482, H:G.484 K.21: 8 residues within 4Å: Chain F: E.482, S.483, G.484, H.486 Chain G: G.313, P.314, G.315, A.318 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain F Metal complexes: G:G.313, G:G.315, G:A.318, F:E.482, F:G.484 K.24: 8 residues within 4Å: Chain E: E.482, S.483, G.484, H.486 Chain H: G.313, P.314, G.315, A.318 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain E Metal complexes: H:G.313, H:G.315, H:A.318, E:E.482, E:G.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imamura, A. et al., Allosteric regulation accompanied by oligomeric state changes of Trypanosoma brucei GMP reductase through cystathionine-beta-synthase domain. Nat Commun (2020)

Release Date

2020-02-26

Peptides

GMP reductase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

GMP reductase

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