SMTL ID : 5fqi.1

W229D and F290W mutant of the last common ancestor of Gram-negative bacteria (GNCA4) beta-lactamase class A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: I.70, T.71, D.76, L.112, E.115 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.71, A:D.76 Water bridges: A:T.71 GOL.2: 9 residues within 4Å: Chain A: A.23, V.24, L.25, R.32, F.33, G.34, A.159, A.162, A.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.24, A:A.163 GOL.3: 6 residues within 4Å: Chain A: G.131, D.132, N.133, V.134, A.160, A.163 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.133, A:N.133, A:V.134 Water bridges: A:D.38, A:G.131, A:T.157, A:T.164

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

EDO.4: 4 residues within 4Å: Chain A: D.60, L.66, A.177, S.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 Water bridges: A:A.177, A:Q.181 EDO.5: 7 residues within 4Å: Chain A: S.45, K.48, Y.80, S.105, N.107, E.141, N.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.48, A:K.48, A:N.107, A:N.145 EDO.6: 3 residues within 4Å: Chain A: R.40, N.133, V.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.40, A:N.133 Water bridges: A:R.40 EDO.7: 4 residues within 4Å: Chain A: D.172, V.173, L.174, S.175 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.60, A:V.173 EDO.8: 4 residues within 4Å: Chain A: F.33, A.262, W.263, H.265 No protein-ligand interaction detected (PLIP) EDO.9: 7 residues within 4Å: Chain A: R.19, R.40, F.41, P.42, P.149, G.150, D.151 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.19, A:G.150 Water bridges: A:D.151, A:D.151, A:T.239 EDO.10: 6 residues within 4Å: Chain A: R.69, H.87, D.90, G.91, M.92, E.96 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.69, A:R.69, A:D.90, A:D.90, A:E.96 EDO.11: 4 residues within 4Å: Chain A: Q.180, V.183, R.205, W.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.180, A:R.205 EDO.12: 3 residues within 4Å: Chain A: R.68, E.115 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.115, A:E.115 Water bridges: A:R.68

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.13: 4 residues within 4Å: Chain A: L.12, A.250, V.251, E.254 No protein-ligand interaction detected (PLIP)

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

PEG.14: 2 residues within 4Å: Chain A: R.15, Q.242 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.15: 3 residues within 4Å: Chain A: D.193, K.194, A.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.194

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.16: 6 residues within 4Å: Chain A: L.169, L.170, P.176, R.179, Q.180, V.183 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.170, A:R.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Risso, V.A. et al., De novo active sites for resurrected Precambrian enzymes. Nat Commun (2017)

Release Date

2016-12-21

Peptides

GNCA4 LACTAMASE W229D AND F290W: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GNCA4 LACTAMASE W229D AND F290W

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