SMTL ID : 7bj8.1

Structure of L1 with 2-Mercaptomethyl-thiazolidine D-syn-1b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

4 x QST: (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

QST.1: 15 residues within 4Å: Chain A: Y.13, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.19 Hydrogen bonds: A:Y.13, A:S.189 Salt bridges: A:H.162 QST.6: 15 residues within 4Å: Chain B: Y.13, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.19 Hydrogen bonds: B:Y.13, B:S.189 Salt bridges: B:H.162 QST.11: 15 residues within 4Å: Chain C: Y.13, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.12, ZN.13 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.19 Hydrogen bonds: C:Y.13, C:S.189 Salt bridges: C:H.162 QST.16: 15 residues within 4Å: Chain D: Y.13, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.17, ZN.18 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.19 Hydrogen bonds: D:Y.13, D:S.189 Salt bridges: D:H.162

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.86, D.90, H.91, H.227 Ligands: QST.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.90, A:D.90, A:H.91, A:H.227 ZN.3: 6 residues within 4Å: Chain A: H.86, H.88, H.91, H.162 Ligands: QST.1, ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.86, A:H.88, A:H.162 ZN.7: 6 residues within 4Å: Chain B: H.86, D.90, H.91, H.227 Ligands: QST.6, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.90, B:D.90, B:H.91, B:H.227 ZN.8: 6 residues within 4Å: Chain B: H.86, H.88, H.91, H.162 Ligands: QST.6, ZN.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.86, B:H.88, B:H.162 ZN.12: 6 residues within 4Å: Chain C: H.86, D.90, H.91, H.227 Ligands: QST.11, ZN.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.90, C:D.90, C:H.91, C:H.227 ZN.13: 6 residues within 4Å: Chain C: H.86, H.88, H.91, H.162 Ligands: QST.11, ZN.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.86, C:H.88, C:H.162 ZN.17: 6 residues within 4Å: Chain D: H.86, D.90, H.91, H.227 Ligands: QST.16, ZN.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.90, D:D.90, D:H.91, D:H.227 ZN.18: 6 residues within 4Å: Chain D: H.86, H.88, H.91, H.162 Ligands: QST.16, ZN.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.86, D:H.88, D:H.162

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: R.139, V.146, I.147, T.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.148, A:T.148 Water bridges: A:R.139 Salt bridges: A:R.139 SO4.5: 6 residues within 4Å: Chain A: R.175, A.239, R.240, A.241, G.242, A.243 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.175, A:A.239, A:G.242, A:A.243 Water bridges: A:A.241, A:A.241 SO4.9: 4 residues within 4Å: Chain B: R.139, V.146, I.147, T.148 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.148, B:T.148 Water bridges: B:R.139 Salt bridges: B:R.139 SO4.10: 6 residues within 4Å: Chain B: R.175, A.239, R.240, A.241, G.242, A.243 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.175, B:A.239, B:G.242, B:A.243 Water bridges: B:A.241, B:A.241 SO4.14: 4 residues within 4Å: Chain C: R.139, V.146, I.147, T.148 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.148, C:T.148 Water bridges: C:R.139 Salt bridges: C:R.139 SO4.15: 6 residues within 4Å: Chain C: R.175, A.239, R.240, A.241, G.242, A.243 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.175, C:A.239, C:G.242, C:A.243 Water bridges: C:A.241, C:A.241 SO4.19: 4 residues within 4Å: Chain D: R.139, V.146, I.147, T.148 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.148, D:T.148 Water bridges: D:R.139 Salt bridges: D:R.139 SO4.20: 6 residues within 4Å: Chain D: R.175, A.239, R.240, A.241, G.242, A.243 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.175, D:A.239, D:G.242, D:A.243 Water bridges: D:A.241, D:A.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hinchliffe, P. et al., 2-Mercaptomethyl Thiazolidines (MMTZs) Inhibit All Metallo-beta-Lactamase Classes by Maintaining a Conserved Binding Mode. Acs Infect Dis. (2021)

Release Date

2021-09-15

Peptides

Metallo-beta-lactamase L1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Metallo-beta-lactamase L1

Related Entries With Identical Sequence