SMTL ID : 3u7j.1 (1 other biounit)

Crystal structure of Ribose-5-phosphate isomerase A from Burkholderia thailandensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: K.15, G.41, S.42, T.43, K.133 Ligands: EDO.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.42, A:S.42, A:T.43, A:T.43 Water bridges: A:S.42, A:S.42, A:A.44, A:G.94, A:A.95, A:K.133 Salt bridges: A:K.15, A:K.133 SO4.6: 4 residues within 4Å: Chain A: S.65, V.66, T.69, R.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.65, A:T.69 Water bridges: A:R.114 Salt bridges: A:R.114 SO4.9: 6 residues within 4Å: Chain B: K.15, G.41, S.42, T.43, K.133 Ligands: EDO.10 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.42, B:S.42, B:T.43 Water bridges: B:S.42, B:S.42, B:A.44, B:G.94, B:A.95, B:K.133 Salt bridges: B:K.15, B:K.133 SO4.14: 4 residues within 4Å: Chain B: S.65, V.66, T.69, R.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.65 Water bridges: B:R.114 Salt bridges: B:R.114

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

EDO.2: 10 residues within 4Å: Chain A: T.40, D.93, G.94, A.95, D.96, K.106, G.107, E.115 Ligands: SO4.1, K.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.40, A:G.94, A:D.96, A:G.107 EDO.4: 3 residues within 4Å: Chain A: T.10, D.12, E.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.10, A:D.12 Water bridges: A:D.12 EDO.5: 10 residues within 4Å: Chain A: K.116, E.200, N.204, V.210, T.211, V.212 Chain B: N.204, G.205, W.206, P.207 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.116, A:N.204, A:V.212, A:V.212, B:G.205 EDO.7: 4 residues within 4Å: Chain A: A.154, R.157, R.158 Chain B: V.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.154, A:R.157 EDO.8: 3 residues within 4Å: Chain A: D.195, P.196, R.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.195, A:R.197 Water bridges: A:D.99, A:R.197 EDO.10: 10 residues within 4Å: Chain B: T.40, D.93, G.94, A.95, D.96, K.106, G.107, E.115 Ligands: SO4.9, K.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.40, B:G.94, B:D.96, B:G.107 EDO.12: 3 residues within 4Å: Chain B: T.10, D.12, E.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.10, B:T.10 Water bridges: B:D.12 EDO.13: 10 residues within 4Å: Chain A: N.204, G.205, W.206, P.207 Chain B: K.116, E.200, N.204, V.210, T.211, V.212 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.116, B:E.200, B:N.204, B:V.212, B:V.212, A:G.205 EDO.15: 4 residues within 4Å: Chain A: V.121 Chain B: A.154, R.157, R.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.154, B:R.157 EDO.16: 3 residues within 4Å: Chain B: D.195, P.196, R.197 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.197 Water bridges: B:D.99, B:R.197

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: G.107, G.109, G.110, A.111, E.115 Ligands: EDO.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.115, H2O.5 K.11: 6 residues within 4Å: Chain B: G.107, G.109, G.110, A.111, E.115 Ligands: EDO.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.115, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Combining functional and structural genomics to sample the essential Burkholderia structome. Plos One (2013)

Release Date

2011-11-16

Peptides

Ribose-5-phosphate isomerase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribose-5-phosphate isomerase A

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