SMTL ID : 6tww.1

Variant W229D/F290W-19 of the last common ancestor of Gram-negative bacteria beta-lactamase class A (GNCA4)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

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

FMT.1: 3 residues within 4Å: Chain A: D.243, A.244, R.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.244, A:R.247, A:R.247 Water bridges: A:G.215 FMT.3: 4 residues within 4Å: Chain A: P.81, V.82, K.85, Y.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.81 FMT.5: 3 residues within 4Å: Chain A: G.16, G.17, R.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.16 FMT.6: 4 residues within 4Å: Chain A: R.39, G.149, D.150, P.151 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.39, A:G.149, A:D.150 FMT.7: 2 residues within 4Å: Chain A: R.127, R.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127, A:R.135 FMT.8: 6 residues within 4Å: Chain A: R.68, H.86, D.89, G.90, M.91, E.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.68, A:R.68, A:H.86

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

ACT.2: 6 residues within 4Å: Chain A: P.200, D.203, V.223, P.225, I.231, H.265 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.223, A:I.231 Hydrogen bonds: A:D.203 Salt bridges: A:H.265

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: S.44, K.47, Y.79, S.104, N.106, N.144, T.211 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.44, A:S.44, A:K.47, A:S.104, A:N.106, A:N.144 Water bridges: A:T.209, A:T.211, A:T.211

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: H.228, H.265 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.228, A:H.265, H2O.1, H2O.9, H2O.10, H2O.10

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

NA.10: 2 residues within 4Å: Chain A: Y.71, V.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.71, A:V.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Risso, V.A. et al., Enhancing ade novoenzyme activity by computationally-focused ultra-low-throughput screening. Chem Sci (2020)

Release Date

2020-06-03

Peptides

Beta-Lactamase (GNCA4): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-Lactamase (GNCA4)