SMTL ID : 7atf.1 (1 other biounit)

Structure of EstD11 in complex with p-Nitrophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

11 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: V.44, E.45, L.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.45, A:L.46 FMT.2: 3 residues within 4Å: Chain A: G.226, L.227, P.228 No protein-ligand interaction detected (PLIP) FMT.3: 5 residues within 4Å: Chain A: P.22, T.23, V.24, R.201, M.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.24, A:R.201 FMT.4: 2 residues within 4Å: Chain A: R.84, R.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.87, A:R.87 FMT.5: 6 residues within 4Å: Chain A: T.122, R.126, A.156, L.157, A.160 Ligands: FMT.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.122, A:R.126, A:A.156 FMT.6: 5 residues within 4Å: Chain A: P.115, T.122, A.156, L.216 Ligands: FMT.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.122 FMT.7: 5 residues within 4Å: Chain A: G.52, R.123, R.126, W.127, E.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.123 FMT.8: 2 residues within 4Å: Chain A: E.119, R.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.123 Water bridges: A:R.107, A:R.123 FMT.9: 3 residues within 4Å: Chain A: W.58, R.60, R.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.58, A:R.60, A:R.100 Water bridges: A:R.100 FMT.11: 6 residues within 4Å: Chain A: G.75, G.76, H.86, D.143, S.144 Ligands: NPO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.143 FMT.13: 2 residues within 4Å: Chain A: I.180, R.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.213, A:R.213

1 x NPO: P-NITROPHENOL(Non-covalent)

NPO.10: 13 residues within 4Å: Chain A: L.19, G.75, G.76, G.77, S.144, A.145, W.174, V.194, L.199, M.202, L.240, H.268 Ligands: FMT.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.19, A:W.174, A:W.174, A:L.240

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 3 residues within 4Å: Chain A: E.285, R.286, E.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.289 Water bridges: A:R.286 ACT.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miguel-Ruano, V. et al., Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. Comput Struct Biotechnol J (2021)

Release Date

2021-03-03

Peptides

EstD11: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

EstD11

Related Entries With Identical Sequence