SMTL ID : 2fli.1 (1 other biounit)

The crystal structure of D-ribulose 5-phosphate 3-epimerase from Streptococus pyogenes complexed with D-xylitol 5-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.34, D.36, H.67, D.176 Ligands: DX5.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.34, A:D.36, A:H.67, A:D.176 ZN.3: 5 residues within 4Å: Chain B: H.34, D.36, H.67, D.176 Ligands: DX5.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.34, B:D.36, B:H.67, B:D.176 ZN.5: 5 residues within 4Å: Chain C: H.34, D.36, H.67, D.176 Ligands: DX5.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.34, C:D.36, C:H.67, C:D.176 ZN.7: 5 residues within 4Å: Chain D: H.34, D.36, H.67, D.176 Ligands: DX5.8 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.34, D:D.36, D:H.67, D:D.176 ZN.9: 5 residues within 4Å: Chain E: H.34, D.36, H.67, D.176 Ligands: DX5.10 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.34, E:D.36, E:H.67, E:D.176 ZN.11: 5 residues within 4Å: Chain F: H.34, D.36, H.67, D.176 Ligands: DX5.12 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.34, F:D.36, F:H.67, F:D.176

6 x DX5: D-XYLITOL-5-PHOSPHATE(Non-covalent)

DX5.2: 20 residues within 4Å: Chain A: S.9, L.11, H.34, D.36, M.38, H.67, M.69, P.142, G.143, F.144, G.145, G.146, D.176, G.177, G.178, V.196, A.197, G.198, S.199 Ligands: ZN.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.9, A:D.36, A:G.143, A:G.146, A:G.178, A:G.198, A:S.199 Water bridges: A:Q.147, A:Q.147, A:G.177, A:V.179, A:S.199, A:S.199, A:Y.200, A:Y.200 DX5.4: 19 residues within 4Å: Chain B: S.9, L.11, H.34, D.36, H.67, M.69, P.142, G.143, F.144, G.145, G.146, D.176, G.177, G.178, V.196, A.197, G.198, S.199 Ligands: ZN.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.9, B:D.36, B:G.143, B:F.144, B:G.146, B:G.178, B:G.198, B:S.199 Water bridges: B:Q.147, B:G.177, B:V.179, B:S.199, B:S.199, B:Y.200, B:Y.200 DX5.6: 21 residues within 4Å: Chain C: S.9, L.11, H.34, D.36, M.38, H.67, M.69, M.138, P.142, G.143, F.144, G.145, G.146, D.176, G.177, G.178, V.196, A.197, G.198, S.199 Ligands: ZN.5 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.9, C:D.36, C:G.143, C:G.146, C:G.178, C:G.198, C:S.199 Water bridges: C:Q.147, C:D.176, C:V.196, C:S.199, C:S.199, C:Y.200 DX5.8: 20 residues within 4Å: Chain D: S.9, L.11, H.34, D.36, M.38, H.67, M.69, P.142, G.143, F.144, G.145, G.146, D.176, G.177, G.178, V.196, A.197, G.198, S.199 Ligands: ZN.7 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.9, D:D.36, D:G.143, D:F.144, D:G.146, D:G.178, D:G.198, D:S.199 Water bridges: D:Q.147, D:G.177, D:V.179, D:V.179, D:V.179, D:S.199, D:S.199 DX5.10: 19 residues within 4Å: Chain E: S.9, L.11, H.34, D.36, H.67, M.69, P.142, G.143, F.144, G.145, G.146, D.176, G.177, G.178, V.196, A.197, G.198, S.199 Ligands: ZN.9 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.9, E:D.36, E:G.143, E:F.144, E:F.144, E:G.146, E:D.176, E:G.178, E:G.198, E:S.199 Water bridges: E:Q.147, E:Q.147, E:G.177, E:V.179, E:S.199, E:S.199 DX5.12: 21 residues within 4Å: Chain F: S.9, L.11, H.34, D.36, M.38, H.67, M.69, M.138, P.142, G.143, F.144, G.145, G.146, D.176, G.177, G.178, V.196, A.197, G.198, S.199 Ligands: ZN.11 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:S.9, F:D.36, F:G.143, F:G.146, F:G.178, F:G.198, F:S.199 Water bridges: F:Q.147, F:G.177, F:V.179, F:S.199, F:S.199, F:Y.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akana, J. et al., d-Ribulose 5-Phosphate 3-Epimerase: Functional and Structural Relationships to Members of the Ribulose-Phosphate Binding (beta/alpha)(8)-Barrel Superfamily(,). Biochemistry (2006)

Release Date

2006-03-07

Peptides

ribulose-phosphate 3-epimerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ribulose-phosphate 3-epimerase

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