SMTL ID : 6ty6.1

Variant W229D/F290W-2 of the last common ancestor of Gram-negative bacteria beta-lactamase class A (GNCA4) bound to 5(6)-nitrobenzotriazole (TS-analog)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: P.82, V.83, K.86, Y.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.86, A:Y.104 GOL.7: 6 residues within 4Å: Chain A: G.73, E.75 Chain B: R.19, E.39, R.40 Ligands: FMT.8 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.19, B:R.19, B:R.40 Water bridges: B:R.19, B:R.19, B:R.40, A:E.75 GOL.13: 7 residues within 4Å: Chain B: I.130, G.131, D.132, A.160, A.163, T.164, T.167 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.130, B:A.160, B:T.164, B:T.167 GOL.18: 5 residues within 4Å: Chain B: H.215, G.216, E.240, S.241, Q.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.215, B:E.240 GOL.25: 5 residues within 4Å: Chain B: N.111, E.115, W.140 Chain C: R.136, P.152 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:E.115, B:W.140, C:R.136, C:R.136 Water bridges: B:N.111, B:N.111, B:N.111, B:E.141

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

FMT.2: 8 residues within 4Å: Chain A: S.45, S.105, R.195, K.209, T.210, G.211, T.212 Ligands: FMT.3 Ligand excluded by PLIP FMT.3: 7 residues within 4Å: Chain A: C.44, S.45, N.107, N.145, G.211, T.212 Ligands: FMT.2 Ligand excluded by PLIP FMT.6: 3 residues within 4Å: Chain A: D.38, V.134, T.157 Ligand excluded by PLIP FMT.8: 7 residues within 4Å: Chain A: E.75, D.76 Chain B: R.40, G.150, D.151, P.152 Ligands: GOL.7 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain A: W.140 Chain B: R.136, P.152 Ligand excluded by PLIP FMT.14: 7 residues within 4Å: Chain B: C.44, S.45, N.107, N.145, G.211, T.212 Ligands: FMT.15 Ligand excluded by PLIP FMT.15: 8 residues within 4Å: Chain B: S.45, S.105, R.195, K.209, T.210, G.211, T.212 Ligands: FMT.14 Ligand excluded by PLIP FMT.16: 4 residues within 4Å: Chain B: R.31, A.262, W.263, H.266 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain B: V.78, D.79, P.142 Ligand excluded by PLIP FMT.20: 1 residues within 4Å: Chain B: P.176 Ligand excluded by PLIP FMT.21: 4 residues within 4Å: Chain B: P.82, V.83, K.86, Y.104 Ligand excluded by PLIP FMT.22: 2 residues within 4Å: Chain B: A.261, H.265 Ligand excluded by PLIP FMT.23: 6 residues within 4Å: Chain B: E.115, G.118, G.119, W.140 Chain C: R.136, D.138 Ligand excluded by PLIP FMT.26: 7 residues within 4Å: Chain C: C.44, S.45, N.107, N.145, G.211, T.212 Ligands: FMT.27 Ligand excluded by PLIP FMT.27: 8 residues within 4Å: Chain C: S.45, S.105, R.195, K.209, T.210, G.211, T.212 Ligands: FMT.26 Ligand excluded by PLIP FMT.28: 5 residues within 4Å: Chain A: R.40, P.152 Chain C: D.76, L.112, E.115 Ligand excluded by PLIP FMT.29: 2 residues within 4Å: Chain C: D.203, P.227 Ligand excluded by PLIP

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

ACT.4: 5 residues within 4Å: Chain A: R.40, G.150, D.151, P.152 Chain C: D.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.40 Water bridges: A:R.19, A:R.19, A:R.40 ACT.5: 5 residues within 4Å: Chain A: I.130, G.131, D.132, T.164, T.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.164, A:T.167, A:T.167 ACT.9: 3 residues within 4Å: Chain A: R.136, P.152 Chain C: W.140 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.140 Salt bridges: A:R.136 ACT.19: 4 residues within 4Å: Chain B: I.70, T.71 Chain C: D.38, V.134 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.70 Hydrogen bonds: B:T.71 Water bridges: C:D.38 ACT.30: 6 residues within 4Å: Chain C: I.130, G.131, D.132, A.163, T.164, T.167 1 PLIP interactions: 1 interactions with chain C Water bridges: C:I.130

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

NA.10: 2 residues within 4Å: Chain A: Y.72, V.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.72 Water bridges: A:Y.72

3 x 6NT: 6-NITROBENZOTRIAZOLE(Non-covalent)

6NT.11: 10 residues within 4Å: Chain A: V.24, L.200, D.204, V.224, P.226, I.232, L.234, V.259, V.260, W.263 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.200, A:V.224, A:I.232, A:V.259, A:W.263 Hydrogen bonds: A:D.204 6NT.24: 10 residues within 4Å: Chain B: V.24, L.200, D.204, V.224, P.226, I.232, L.234, V.259, V.260, W.263 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.200, B:V.224, B:I.232, B:V.259, B:V.260, B:W.263 Hydrogen bonds: B:D.204 6NT.31: 9 residues within 4Å: Chain C: V.24, L.200, D.204, V.224, I.232, L.234, V.259, V.260, W.263 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.200, C:V.224, C:I.232, C:V.259, C:V.260, C:W.263 Hydrogen bonds: C:D.204

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 (GNCA4-2): ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Beta lactamase (GNCA4-2)