SMTL ID : 6uac.1

Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with cadmium and hydrolyzed moxolactam

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: G.196, Y.197, E.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.196 EDO.5: 3 residues within 4Å: Chain B: G.196, Y.197, E.270 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.196 EDO.9: 3 residues within 4Å: Chain C: G.196, Y.197, E.270 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.196 EDO.13: 3 residues within 4Å: Chain D: G.196, Y.197, E.270 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.196

8 x CD: CADMIUM ION(Non-covalent)

CD.2: 5 residues within 4Å: Chain A: D.94, H.95, H.231 Ligands: CD.3, MX1.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.94, A:H.95, A:H.231, H2O.1 CD.3: 5 residues within 4Å: Chain A: H.90, H.92, H.166 Ligands: CD.2, MX1.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.90, A:H.92, A:H.166, H2O.1 CD.6: 5 residues within 4Å: Chain B: D.94, H.95, H.231 Ligands: CD.7, MX1.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.94, B:H.95, B:H.231, H2O.10 CD.7: 5 residues within 4Å: Chain B: H.90, H.92, H.166 Ligands: CD.6, MX1.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.90, B:H.92, B:H.166, H2O.10 CD.10: 5 residues within 4Å: Chain C: D.94, H.95, H.231 Ligands: CD.11, MX1.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.94, C:H.95, C:H.231, H2O.20 CD.11: 5 residues within 4Å: Chain C: H.90, H.92, H.166 Ligands: CD.10, MX1.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.90, C:H.92, C:H.166, H2O.20 CD.14: 5 residues within 4Å: Chain D: D.94, H.95, H.231 Ligands: CD.15, MX1.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.94, D:H.95, D:H.231, H2O.29 CD.15: 5 residues within 4Å: Chain D: H.90, H.92, H.166 Ligands: CD.14, MX1.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.90, D:H.92, D:H.166, H2O.29

4 x MX1: (2R)-2-((R)-CARBOXY{[CARBOXY(4-HYDROXYPHENYL)ACETYL]AMINO}METHOXYMETHYL)-5-METHYLENE-5,6-DIHYDRO-2H-1,3-OXAZINE-4-CARBO XYLIC ACID(Non-covalent)

MX1.4: 16 residues within 4Å: Chain A: Y.17, W.23, H.90, H.92, D.94, H.95, F.130, G.133, I.134, H.166, S.191, S.193, P.195, H.231 Ligands: CD.2, CD.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.130, A:F.130, A:I.134, A:P.195 Hydrogen bonds: A:Y.17, A:G.133, A:S.191, A:S.193, A:S.193 Water bridges: A:G.133 Salt bridges: A:H.90, A:H.92, A:H.166, A:H.166, A:H.231 pi-Stacking: A:Y.17 MX1.8: 16 residues within 4Å: Chain B: Y.17, W.23, H.90, H.92, D.94, H.95, F.130, G.133, I.134, H.166, S.191, S.193, P.195, H.231 Ligands: CD.6, CD.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.130, B:F.130, B:I.134, B:P.195 Hydrogen bonds: B:Y.17, B:G.133, B:S.191, B:S.193, B:S.193 Water bridges: B:G.133 Salt bridges: B:H.90, B:H.92, B:H.166, B:H.166, B:H.231 pi-Stacking: B:Y.17 MX1.12: 16 residues within 4Å: Chain C: Y.17, W.23, H.90, H.92, D.94, H.95, F.130, G.133, I.134, H.166, S.191, S.193, P.195, H.231 Ligands: CD.10, CD.11 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.130, C:F.130, C:I.134, C:P.195 Hydrogen bonds: C:G.133, C:S.191, C:S.193, C:S.193 Water bridges: C:G.133 Salt bridges: C:H.90, C:H.92, C:H.166, C:H.166, C:H.231 pi-Stacking: C:Y.17 MX1.16: 16 residues within 4Å: Chain D: Y.17, W.23, H.90, H.92, D.94, H.95, F.130, G.133, I.134, H.166, S.191, S.193, P.195, H.231 Ligands: CD.14, CD.15 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:F.130, D:F.130, D:I.134, D:P.195 Hydrogen bonds: D:G.133, D:S.191, D:S.193, D:S.193 Water bridges: D:H.92, D:H.92, D:G.133 Salt bridges: D:H.90, D:H.92, D:H.166, D:H.166, D:H.231 pi-Stacking: D:Y.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with cadmium and hydrolyzed moxolactam. To Be Published

Release Date

2019-09-25

Peptides

Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)

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