SMTL ID : 5umf.1

Crystal Structure of a Ribulose-phosphate 3-epimerase from Neisseria gonorrhoeae with bound phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.42, D.44, H.75, D.188 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.42, A:D.44, A:H.75, A:D.188 ZN.4: 4 residues within 4Å: Chain B: H.42, D.44, H.75, D.188 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.42, B:D.44, B:H.75, B:D.188 ZN.8: 4 residues within 4Å: Chain C: H.42, D.44, H.75, D.188 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.42, C:D.44, C:H.75, C:D.188 ZN.11: 4 residues within 4Å: Chain D: H.42, D.44, H.75, D.188 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.42, D:D.44, D:H.75, D:D.188 ZN.14: 4 residues within 4Å: Chain E: H.42, D.44, H.75, D.188 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.42, E:D.44, E:H.75, E:D.188 ZN.18: 4 residues within 4Å: Chain F: H.42, D.44, H.75, D.188 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.42, F:D.44, F:H.75, F:D.188

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: S.20, G.153, G.154, G.189, G.190, A.209, G.210, S.211 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.20, A:G.154, A:G.190, A:G.210, A:S.211 Water bridges: A:S.17, A:S.17, A:S.17, A:Q.155, A:G.189, A:I.191, A:S.211, A:S.211, A:A.212 PO4.5: 7 residues within 4Å: Chain B: G.153, G.154, G.189, G.190, A.209, G.210, S.211 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.20, B:G.154, B:G.190, B:G.210, B:S.211 Water bridges: B:S.17, B:S.17, B:S.17, B:Q.155, B:G.189, B:I.191, B:S.211, B:S.211, B:A.212 PO4.9: 8 residues within 4Å: Chain C: S.20, G.153, G.154, G.189, G.190, A.209, G.210, S.211 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.20, C:S.20, C:G.154, C:G.190, C:G.210, C:S.211 Water bridges: C:S.17, C:S.17, C:Q.155, C:G.189, C:I.191, C:S.211, C:S.211, C:A.212 PO4.12: 8 residues within 4Å: Chain D: S.20, G.153, G.154, G.189, G.190, A.209, G.210, S.211 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.20, D:G.154, D:G.190, D:G.210, D:S.211 Water bridges: D:S.17, D:S.17, D:S.17, D:Q.155, D:G.189, D:I.191, D:S.211, D:S.211, D:A.212 PO4.15: 7 residues within 4Å: Chain E: G.153, G.154, G.189, G.190, A.209, G.210, S.211 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.20, E:G.154, E:G.190, E:G.210, E:S.211 Water bridges: E:S.17, E:S.17, E:S.17, E:Q.155, E:G.189, E:I.191, E:S.211, E:S.211, E:A.212 PO4.19: 8 residues within 4Å: Chain F: S.20, G.153, G.154, G.189, G.190, A.209, G.210, S.211 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.20, F:S.20, F:G.154, F:G.190, F:G.210, F:S.211 Water bridges: F:S.17, F:S.17, F:Q.155, F:G.189, F:I.191, F:S.211, F:S.211, F:A.212

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: A.31, N.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:N.32 GOL.6: 5 residues within 4Å: Chain B: N.32, P.217, D.218, Y.219, K.220 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.219, B:K.220 Water bridges: B:P.217, B:D.218, B:D.218, B:Y.219, B:Y.219, B:K.220 GOL.7: 2 residues within 4Å: Chain B: A.31, N.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.32, B:N.32 Water bridges: B:E.28 GOL.10: 2 residues within 4Å: Chain C: A.31, N.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.32, C:N.32 GOL.13: 2 residues within 4Å: Chain D: A.31, N.32 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.32, D:N.32 GOL.16: 5 residues within 4Å: Chain E: N.32, P.217, D.218, Y.219, K.220 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:D.218, E:Y.219, E:K.220 Water bridges: E:N.32, E:P.217, E:D.218, E:D.218, E:Y.219, E:K.220 GOL.17: 2 residues within 4Å: Chain E: A.31, N.32 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.32, E:N.32 GOL.20: 2 residues within 4Å: Chain F: A.31, N.32 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.32, F:N.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of a Ribulose-phosphate 3-epimerase from Neisseria gonorrhoeae with bound phosphate. to be published

Release Date

2017-02-15

Peptides

Ribulose-phosphate 3-epimerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Ribulose-phosphate 3-epimerase