SMTL ID : 5esr.1

Crystal structure of haloalkane dehalogenase (DccA) from Caulobacter crescentus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

12 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: D.238, H.303, H.305 Chain B: E.138, H.308 6 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.308, A:D.238, A:D.238, A:H.303, A:H.305, H2O.9 CO.2: 3 residues within 4Å: Chain A: H.304, H.306 Chain B: H.307 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.307, A:H.304, A:H.306, H2O.10, H2O.10, H2O.11 CO.3: 1 residues within 4Å: Chain A: E.25 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.25, A:E.25, H2O.11, H2O.12, H2O.12 CO.5: 4 residues within 4Å: Chain A: T.243, F.245, E.256, T.273 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.256, H2O.2, H2O.3, H2O.5, H2O.14 CO.6: 6 residues within 4Å: Chain A: E.55, D.123, W.124, F.160, W.163 Ligands: CL.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.123, A:D.123, H2O.10, H2O.12 CO.7: 4 residues within 4Å: Chain A: A.20, H.22, D.40, E.41 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.22, A:D.40, H2O.2, H2O.11, H2O.11 CO.10: 5 residues within 4Å: Chain A: E.138, H.308 Chain B: D.238, H.303, H.305 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.238, B:D.238, B:H.303, B:H.305, A:H.308, H2O.26 CO.11: 3 residues within 4Å: Chain A: H.307 Chain B: H.304, H.306 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.304, B:H.306, A:H.307, H2O.27, H2O.27, H2O.28 CO.12: 1 residues within 4Å: Chain B: E.25 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.25, B:E.25, H2O.28, H2O.29, H2O.29 CO.14: 4 residues within 4Å: Chain B: T.243, F.245, E.256, T.273 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.256, H2O.19, H2O.20, H2O.23, H2O.31 CO.15: 6 residues within 4Å: Chain B: E.55, D.123, W.124, F.160, W.163 Ligands: CL.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.123, B:D.123, H2O.27, H2O.29 CO.16: 4 residues within 4Å: Chain B: A.20, H.22, D.40, E.41 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.22, B:D.40, H2O.19, H2O.28, H2O.28

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: N.180, T.183, R.185, D.186, L.187 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.180, A:T.183, A:T.183, A:R.185, H2O.5 MG.8: 3 residues within 4Å: Chain A: K.72, H.74, D.293 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.293, H2O.8, H2O.10, H2O.14 MG.13: 5 residues within 4Å: Chain B: N.180, T.183, R.185, D.186, L.187 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.180, B:T.183, B:T.183, B:R.185, H2O.22 MG.17: 3 residues within 4Å: Chain B: K.72, H.74, D.293 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.293, H2O.25, H2O.27, H2O.31

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

CL.9: 8 residues within 4Å: Chain A: E.55, W.124, F.160, W.163, F.211, P.212, V.215 Ligands: CO.6 Ligand excluded by PLIP CL.18: 8 residues within 4Å: Chain B: E.55, W.124, F.160, W.163, F.211, P.212, V.215 Ligands: CO.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carlucci, L. et al., Biochemical characterization of two haloalkane dehalogenases: DccA from Caulobacter crescentus and DsaA from Saccharomonospora azurea. Protein Sci. (2016)

Release Date

2016-06-01

Peptides

Haloalkane dehalogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Haloalkane dehalogenase