SMTL ID : 3qc3.1

Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.36, D.38, H.71, D.176 Ligands: NI.2, FE.3, GOL.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.36, A:D.38, A:H.71, A:D.176, H2O.3 ZN.5: 7 residues within 4Å: Chain B: H.36, D.38, H.71, D.176 Ligands: NI.6, FE.7, GOL.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.36, B:D.38, B:H.71, B:D.176, H2O.7

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 7 residues within 4Å: Chain A: H.36, D.38, H.71, D.176 Ligands: ZN.1, FE.3, GOL.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.36, A:D.38, A:H.71, A:D.176, H2O.3 NI.6: 7 residues within 4Å: Chain B: H.36, D.38, H.71, D.176 Ligands: ZN.5, FE.7, GOL.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.36, B:D.38, B:H.71, B:D.176, H2O.7

2 x FE: FE (III) ION(Non-covalent)

FE.3: 7 residues within 4Å: Chain A: H.36, D.38, H.71, D.176 Ligands: ZN.1, NI.2, GOL.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.36, A:D.38, A:H.71, A:D.176, H2O.3 FE.7: 7 residues within 4Å: Chain B: H.36, D.38, H.71, D.176 Ligands: ZN.5, NI.6, GOL.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.36, B:D.38, B:H.71, B:D.176, H2O.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: D.38, M.40, H.71, M.73, M.142, V.144, P.146, G.147, D.176 Ligands: ZN.1, NI.2, FE.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.147, A:D.176 Water bridges: A:G.178 GOL.8: 12 residues within 4Å: Chain B: D.38, M.40, H.71, M.73, M.142, V.144, P.146, G.147, D.176 Ligands: ZN.5, NI.6, FE.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.147, B:F.148 Water bridges: B:F.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution. To be published

Release Date

2011-03-09

Peptides

D-ribulose-5-phosphate-3-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-ribulose-5-phosphate-3-epimerase