SMTL ID : 3qd5.2 (1 other biounit)

Crystal structure of a putative ribose-5-phosphate isomerase from Coccidioides immitis solved by combined iodide ion SAD and MR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.75, I.111, D.115, A.116, Q.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.75, A:D.115 Water bridges: A:F.143 EDO.15: 6 residues within 4Å: Chain B: R.75, I.111, D.115, A.116, Q.117, F.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.75, B:D.115 Water bridges: B:F.143 EDO.32: 5 residues within 4Å: Chain C: R.75, I.111, D.115, A.116, Q.117 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.75 Water bridges: C:F.143 EDO.46: 6 residues within 4Å: Chain D: R.75, I.111, D.115, A.116, Q.117, F.143 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.75 Water bridges: D:F.143

58 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 3 residues within 4Å: Chain A: T.8, P.38 Ligands: IOD.3 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: P.9, L.39 Ligands: IOD.2 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Ligands: IOD.5 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.142 Ligands: IOD.4 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: C.80, T.82, G.85 Chain B: N.114 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: G.81 Chain B: F.105 Ligands: IOD.8 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: G.81, R.124 Ligands: IOD.7 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: Y.26 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: H.33, K.132 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: A.56, H.59 Chain B: A.155 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: Q.66 Chain B: Y.159 Ligand excluded by PLIP IOD.13: 5 residues within 4Å: Chain A: D.103, T.104 Chain C: D.103, T.104 Ligands: IOD.44 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: R.14 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: F.105 Chain B: R.124 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain B: P.9, L.39 Ligands: IOD.31 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain B: Y.26 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain B: K.132 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain B: K.31 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain B: K.31 Ligand excluded by PLIP IOD.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain B: T.49, S.50, T.52, D.53 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain B: D.21 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain B: T.55, A.56 Ligand excluded by PLIP IOD.26: 5 residues within 4Å: Chain B: D.103, T.104 Chain D: D.103, T.104 Ligands: IOD.57 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain B: H.33, K.132 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain B: D.144, Q.145, K.146 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain B: Y.159 Ligand excluded by PLIP IOD.30: 1 residues within 4Å: Chain B: G.47 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain B: T.8 Ligands: IOD.17 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain C: T.8, P.38 Ligands: IOD.34 Ligand excluded by PLIP IOD.34: 3 residues within 4Å: Chain C: P.9, L.39 Ligands: IOD.33 Ligand excluded by PLIP IOD.35: 1 residues within 4Å: Ligands: IOD.36 Ligand excluded by PLIP IOD.36: 2 residues within 4Å: Chain C: R.142 Ligands: IOD.35 Ligand excluded by PLIP IOD.37: 4 residues within 4Å: Chain C: C.80, T.82, G.85 Chain D: N.114 Ligand excluded by PLIP IOD.38: 3 residues within 4Å: Chain C: G.81 Chain D: F.105 Ligands: IOD.39 Ligand excluded by PLIP IOD.39: 3 residues within 4Å: Chain C: G.81, R.124 Ligands: IOD.38 Ligand excluded by PLIP IOD.40: 1 residues within 4Å: Chain C: Y.26 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain C: H.33, K.132 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain C: A.56, H.59 Chain D: A.155 Ligand excluded by PLIP IOD.43: 2 residues within 4Å: Chain C: Q.66 Chain D: Y.159 Ligand excluded by PLIP IOD.44: 5 residues within 4Å: Chain A: D.103, T.104 Chain C: D.103, T.104 Ligands: IOD.13 Ligand excluded by PLIP IOD.45: 1 residues within 4Å: Chain C: R.14 Ligand excluded by PLIP IOD.47: 2 residues within 4Å: Chain C: F.105 Chain D: R.124 Ligand excluded by PLIP IOD.48: 3 residues within 4Å: Chain D: P.9, L.39 Ligands: IOD.62 Ligand excluded by PLIP IOD.49: 1 residues within 4Å: Chain D: Y.26 Ligand excluded by PLIP IOD.50: 1 residues within 4Å: Chain D: K.132 Ligand excluded by PLIP IOD.51: 1 residues within 4Å: Chain D: K.31 Ligand excluded by PLIP IOD.52: 1 residues within 4Å: Chain D: K.31 Ligand excluded by PLIP IOD.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.54: 4 residues within 4Å: Chain D: T.49, S.50, T.52, D.53 Ligand excluded by PLIP IOD.55: 1 residues within 4Å: Chain D: D.21 Ligand excluded by PLIP IOD.56: 2 residues within 4Å: Chain D: T.55, A.56 Ligand excluded by PLIP IOD.57: 5 residues within 4Å: Chain B: D.103, T.104 Chain D: D.103, T.104 Ligands: IOD.26 Ligand excluded by PLIP IOD.58: 2 residues within 4Å: Chain D: H.33, K.132 Ligand excluded by PLIP IOD.59: 3 residues within 4Å: Chain D: D.144, Q.145, K.146 Ligand excluded by PLIP IOD.60: 1 residues within 4Å: Chain D: Y.159 Ligand excluded by PLIP IOD.61: 1 residues within 4Å: Chain D: G.47 Ligand excluded by PLIP IOD.62: 2 residues within 4Å: Chain D: T.8 Ligands: IOD.48 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

2011-02-09

Peptides

putative ribose-5-phosphate isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

putative ribose-5-phosphate isomerase

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