SMTL ID : 4lxi.1

Crystal Structure of the S105A mutant of a carbon-carbon bond hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with 5,8-diF HOPDA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

2 x 22J: (3E,5R)-5-fluoro-6-(2-fluorophenyl)-2,6-dioxohex-3-enoic acid(Non-covalent)

22J.1: 18 residues within 4Å: Chain A: G.33, G.34, G.35, A.38, N.43, N.104, A.105, M.106, V.149, M.150, L.166, R.180, M.197, L.205, M.229, V.230, H.255, W.256 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.105, A:L.166, A:L.205 Hydrogen bonds: A:G.33, A:G.34, A:G.35, A:N.43, A:N.43, A:N.104, A:M.106 Salt bridges: A:R.180 22J.3: 18 residues within 4Å: Chain B: G.33, G.34, G.35, A.38, N.43, N.104, A.105, M.106, V.149, M.150, L.166, R.180, M.197, L.205, M.229, V.230, H.255, W.256 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.105, B:L.166, B:L.205 Hydrogen bonds: B:G.33, B:G.34, B:G.35, B:N.43, B:N.43, B:N.104, B:M.106 Salt bridges: B:R.180

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

NA.2: 2 residues within 4Å: Chain A: A.164, T.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.167 NA.4: 2 residues within 4Å: Chain B: A.164, T.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruzzini, A.C. et al., A substrate-assisted mechanism of nucleophile activation in a ser-his-asp containing C-C bond hydrolase. Biochemistry (2013)

Release Date

2013-10-09

Peptides

MCP Hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

MCP Hydrolase

Related Entries With Identical Sequence