SMTL ID : 3c5y.2 (3 other biounits)

Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: F.108, N.125, R.174, L.177, R.178 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: P.105, K.181, D.182, C.185, R.186, D.187 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: R.166, I.169, M.170, N.173 Chain B: E.27, Y.68 Ligands: EDO.12 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: K.33, S.135, F.138 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Y.162, P.163, R.164, E.165 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain B: F.119, K.152 Chain D: L.144 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: F.108, N.125, R.174, L.177, R.178 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: I.124, M.170 Chain B: S.29, C.91, G.92 Chain C: W.140 Ligands: EDO.3 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: N.28, S.29, Q.30, A.31, A.32, K.33 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: F.53, E.211, L.212, N.216 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: M.70, D.198, L.199, A.202 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain C: F.108, N.125, R.174, L.177, R.178 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: L.144 Chain C: F.119, K.152 Ligands: EDO.23 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: W.140 Chain C: E.27, S.29, Y.68, C.91, G.92 Chain D: R.166 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: I.113, N.145 Chain C: D.114 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain C: F.53, E.211, L.212, P.215, N.216 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: L.144 Chain C: F.119, Y.162 Ligands: EDO.19 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: T.194, V.195, D.196, Q.197 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain D: F.108, N.125, R.174, L.177, R.178 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain C: R.186 Chain D: P.105, D.182, C.185 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: I.113, N.145 Chain D: D.114 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain A: W.140 Chain C: R.166 Chain D: E.27, S.29, Y.68, C.91, G.92 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain D: D.196, Q.197, D.198 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: Y.162 Chain D: F.138, G.139, W.140, A.141, E.143 Ligand excluded by PLIP

6 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 5 residues within 4Å: Chain B: Y.214, P.215, R.227 Ligands: NO3.7, NO3.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.227 Water bridges: B:R.227 NO3.7: 2 residues within 4Å: Chain B: P.215 Ligands: NO3.6 No protein-ligand interaction detected (PLIP) NO3.8: 4 residues within 4Å: Chain B: A.210, Y.214, R.227 Ligands: NO3.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.227, B:R.227 NO3.9: 6 residues within 4Å: Chain B: Q.18, G.19, M.20, G.49, H.50, K.51 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.18, B:G.19, B:G.49, B:K.51, B:K.51 NO3.16: 4 residues within 4Å: Chain C: Y.214, P.215, R.227 Ligands: NO3.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.227 Water bridges: C:Y.214, C:P.215, C:R.227 NO3.17: 4 residues within 4Å: Chain C: A.210, Y.214, R.227 Ligands: NO3.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.227, C:R.227 Water bridges: C:Y.214, C:Y.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative ribose 5-phosphate isomerase (YP_001165900.1) from Novosphingobium aromaticivorans DSM 12444 at 1.81 A resolution. To be published

Release Date

2008-02-19

Peptides

Ribose/galactose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Ribose/galactose isomerase

Related Entries With Identical Sequence