SMTL ID : 2x5x.1

The crystal structure of PhaZ7 at atomic (1.2 Angstrom) resolution reveals details of the active site and suggests a substrate binding mode

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

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

IOD.1: 4 residues within 4Å: Chain A: G.20, G.34, S.35 Ligands: NA.15 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: R.228, A.230 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: P.24, G.25 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: V.26, G.27 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: A.340, A.341 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: C.3, N.6 Ligand excluded by PLIP IOD.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.19: 4 residues within 4Å: Chain B: G.20, G.34, S.35 Ligands: NA.33 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain B: R.228, A.230 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain B: P.24, G.25 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain B: V.26, G.27 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain B: A.340, A.341 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain B: C.3, N.6 Ligand excluded by PLIP IOD.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x SO2: SULFUR DIOXIDE(Covalent)

SO2.7: 9 residues within 4Å: Chain A: G.48, N.49, H.135, S.136, M.137, V.244, M.291, H.306, F.307 No protein-ligand interaction detected (PLIP) SO2.25: 9 residues within 4Å: Chain B: G.48, N.49, H.135, S.136, M.137, V.244, M.291, H.306, F.307 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 6 residues within 4Å: Chain A: Y.105, Y.176, G.185, S.186, Q.187, N.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.186 Water bridges: A:N.188, A:N.188 PG4.26: 6 residues within 4Å: Chain B: Y.105, Y.176, G.185, S.186, Q.187, N.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.186 Water bridges: B:N.188, B:N.188

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

CL.9: 2 residues within 4Å: Chain A: Y.204, G.205 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: G.99, A.101, G.290, M.291 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: P.292, N.294, A.295 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: N.62, G.65, Y.66, G.67 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: N.83, D.84 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: W.202, Y.204 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: Y.204, G.205 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: G.99, A.101, G.290, M.291 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: P.292, N.294, A.295 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain B: N.62, G.65, Y.66, G.67 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain B: N.83, D.84 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: W.202, Y.204 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.15: 2 residues within 4Å: Chain A: G.20 Ligands: IOD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.20 NA.16: 5 residues within 4Å: Chain A: Y.173, Y.204, S.250, F.251, D.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.204, A:S.250 NA.33: 2 residues within 4Å: Chain B: G.20 Ligands: IOD.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.20 NA.34: 5 residues within 4Å: Chain B: Y.173, Y.204, S.250, F.251, D.284 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.250, B:S.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wakadkar, S. et al., The structure of PhaZ7 at atomic (1.2 A) resolution reveals details of the active site and suggests a substrate-binding mode. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. (2010)

Release Date

2010-06-09

Peptides

PHB DEPOLYMERASE PHAZ7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PHB DEPOLYMERASE PHAZ7

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