SMTL ID : 3ovq.1

Crystal Structure of hRPE and D-Ribulose-5-Phospate Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: H.35, D.37, H.70, D.175 Ligands: 5RP.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.35, A:D.37, A:H.70, A:D.175 FE2.7: 5 residues within 4Å: Chain B: H.35, D.37, H.70, D.175 Ligands: 5RP.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.35, B:D.37, B:H.70, B:D.175

2 x 5RP: RIBULOSE-5-PHOSPHATE(Non-covalent)

5RP.2: 18 residues within 4Å: Chain A: S.10, H.35, D.37, M.39, H.70, M.72, P.145, G.146, F.147, G.148, G.149, D.175, G.176, G.177, S.196, G.197, S.198 Ligands: FE2.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.10, A:G.146, A:F.147, A:F.147, A:G.149, A:G.177, A:G.197, A:S.198 Water bridges: A:N.13, A:Q.150, A:G.176, A:V.178, A:A.199 5RP.8: 20 residues within 4Å: Chain B: S.10, L.12, H.35, D.37, M.39, H.70, M.72, M.141, P.145, G.146, F.147, G.148, G.149, D.175, G.176, G.177, S.196, G.197, S.198 Ligands: FE2.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.10, B:G.146, B:F.147, B:F.147, B:G.149, B:G.177, B:G.197, B:S.198, B:S.198 Water bridges: B:Q.150, B:Q.150, B:G.176, B:V.178, B:A.199

7 x XPE: 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL(Non-covalent)

XPE.3: 5 residues within 4Å: Chain A: K.6, D.32, F.66, D.171, M.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.6 XPE.4: 7 residues within 4Å: Chain A: R.58, F.66, G.87, A.88, N.89, G.112, K.114 No protein-ligand interaction detected (PLIP) XPE.5: 5 residues within 4Å: Chain A: M.157, P.158, H.161, W.162, E.188 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.162 XPE.6: 3 residues within 4Å: Chain A: N.100, P.130, W.131 No protein-ligand interaction detected (PLIP) XPE.9: 5 residues within 4Å: Chain B: K.6, D.32, F.66, D.171, M.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.6 XPE.10: 5 residues within 4Å: Chain B: L.95, E.96, G.122, T.123, Y.127 No protein-ligand interaction detected (PLIP) XPE.11: 5 residues within 4Å: Chain B: F.66, G.87, A.88, N.89, G.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.87, B:N.89 Water bridges: B:R.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, W.G. et al., Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE. Faseb J. (2011)

Release Date

2011-03-09

Peptides

Ribulose-phosphate 3-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribulose-phosphate 3-epimerase

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