SMTL ID : 5xtu.1

Crystal Structure of GDSL Esterase of Photobacterium sp. J15

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: A.90, G.91, A.94, K.95, A.97 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.87, A:G.91

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

CL.2: 6 residues within 4Å: Chain A: T.39, G.130, T.131, W.133, R.173, K.177 Ligand excluded by PLIP

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 9 residues within 4Å: Chain A: K.51, R.69, G.137, D.147, N.193, W.196, F.197 Ligands: CA.5, PO4.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.51, A:K.51, A:R.69, A:D.147, A:N.193 CAC.4: 1 residues within 4Å: Chain A: H.122 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: N.193, H.337 Ligands: CAC.3, PO4.7 No protein-ligand interaction detected (PLIP)

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

EDO.6: 5 residues within 4Å: Chain A: G.245, Q.246, Q.247, K.248, K.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.248, A:K.249 Water bridges: A:G.245, A:Q.247

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

PO4.7: 9 residues within 4Å: Chain A: D.43, S.44, G.136, G.137, T.192, N.193, H.337 Ligands: CAC.3, CA.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.44, A:G.137, A:N.193, A:N.193 Salt bridges: A:H.337 PO4.8: 3 residues within 4Å: Chain A: Q.326, N.328, R.329 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.328 Water bridges: A:Q.326, A:Q.326, A:R.329, A:R.329, A:R.329 Salt bridges: A:R.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazlan, S.N.H.S. et al., Crystallization and structure elucidation of GDSL esterase of Photobacterium sp. J15. Int. J. Biol. Macromol. (2018)

Release Date

2018-10-10

Peptides

GDSL-family esterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GDSL-family esterase