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

Crystal structure of a ribose-5-phosphate isomerase B RpiB from Coccidioides immitis bound to phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: Y.74 Chain D: S.130, S.166, K.169 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.130 Water bridges: D:R.126, D:R.126, D:S.130, D:N.131, A:Y.74 Salt bridges: D:K.169 PO4.5: 4 residues within 4Å: Chain B: Y.74 Chain C: S.130, S.166, K.169 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.130 Water bridges: C:R.126, C:R.126, C:S.130, C:N.131, B:Y.74 Salt bridges: C:K.169 PO4.9: 4 residues within 4Å: Chain B: S.130, S.166, K.169 Chain C: Y.74 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.130 Water bridges: B:R.126, B:R.126, B:S.130, B:N.131, C:Y.74 Salt bridges: B:K.169 PO4.13: 4 residues within 4Å: Chain A: S.130, S.166, K.169 Chain D: Y.74 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.130 Water bridges: A:R.126, A:R.126, A:S.130, A:N.131, A:N.131 Salt bridges: A:K.169

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

EDO.2: 6 residues within 4Å: Chain A: R.92, I.128, D.132, A.133, Q.134, F.160 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.92, A:D.132 Water bridges: A:F.160 EDO.3: 5 residues within 4Å: Chain A: K.109, F.180 Chain D: K.109, F.180 Ligands: EDO.15 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.109, A:K.109 EDO.6: 6 residues within 4Å: Chain B: R.92, I.128, D.132, A.133, Q.134, F.160 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.92 Water bridges: B:F.160 EDO.7: 5 residues within 4Å: Chain B: K.109, F.180 Chain C: K.109, F.180 Ligands: EDO.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.109, C:K.109 Water bridges: B:E.177, C:E.177 EDO.10: 6 residues within 4Å: Chain C: R.92, I.128, D.132, A.133, Q.134, F.160 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.92 Water bridges: C:F.160 EDO.11: 5 residues within 4Å: Chain B: K.109, F.180 Chain C: K.109, F.180 Ligands: EDO.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.109, C:K.109 Water bridges: B:E.177, C:E.177 EDO.14: 6 residues within 4Å: Chain D: R.92, I.128, D.132, A.133, Q.134, F.160 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.92, D:D.132 Water bridges: D:F.160 EDO.15: 5 residues within 4Å: Chain A: K.109, F.180 Chain D: K.109, F.180 Ligands: EDO.3 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.109, A:K.109

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: D.120, T.121 Chain C: D.120, T.121 Ligands: CL.12 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: D.120, T.121 Chain D: D.120, T.121 Ligands: CL.16 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: D.120, T.121 Chain C: D.120, T.121 Ligands: CL.4 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: D.120, T.121 Chain D: D.120, T.121 Ligands: CL.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis. Bmc Struct.Biol. (2011)

Release Date

2011-06-22

Peptides

ribose 5-phosphate isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

ribose 5-phosphate isomerase

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