SMTL ID : 6v54.1

Crystal Structure of Metallo Beta Lactamase from Hirschia baltica

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

FMT.2: 8 residues within 4Å: Chain A: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.5, ZN.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.185 Water bridges: A:R.176, A:R.176, A:R.176, A:N.185 FMT.9: 3 residues within 4Å: Chain A: D.54, Y.55, R.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.84, A:R.84 FMT.11: 8 residues within 4Å: Chain B: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.14, ZN.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.185 Water bridges: B:R.176, B:R.176, B:R.176, B:N.185 FMT.18: 3 residues within 4Å: Chain B: D.54, Y.55, R.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.84, B:R.84 FMT.20: 8 residues within 4Å: Chain C: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.23, ZN.24 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.185 Water bridges: C:R.176, C:R.176, C:R.176, C:N.185 FMT.27: 3 residues within 4Å: Chain C: D.54, Y.55, R.84 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.84, C:R.84 FMT.29: 8 residues within 4Å: Chain D: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.32, ZN.33 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.185 Water bridges: D:H.92, D:R.176, D:R.176, D:R.176, D:N.185 FMT.36: 3 residues within 4Å: Chain D: D.54, Y.55, R.84 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.84, D:R.84 FMT.38: 8 residues within 4Å: Chain E: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.41, ZN.42 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.185 Water bridges: E:R.176, E:R.176, E:R.176, E:N.185 FMT.45: 3 residues within 4Å: Chain E: D.54, Y.55, R.84 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.84, E:R.84 FMT.47: 8 residues within 4Å: Chain F: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.50, ZN.51 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.185 Water bridges: F:R.176, F:R.176, F:R.176, F:N.185 FMT.54: 3 residues within 4Å: Chain F: D.54, Y.55, R.84 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.84, F:R.84

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

EDO.3: 5 residues within 4Å: Chain A: T.26, G.27, E.51, E.163, V.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.51 EDO.12: 5 residues within 4Å: Chain B: T.26, G.27, E.51, E.163, V.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.51 EDO.21: 5 residues within 4Å: Chain C: T.26, G.27, E.51, E.163, V.165 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.51 EDO.30: 5 residues within 4Å: Chain D: T.26, G.27, E.51, E.163, V.165 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.51 EDO.39: 5 residues within 4Å: Chain E: T.26, G.27, E.51, E.163, V.165 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.51 EDO.48: 5 residues within 4Å: Chain F: T.26, G.27, E.51, E.163, V.165 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.51

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: P.177, G.216, K.217 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: P.177, G.216, K.217 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: P.177, G.216, K.217 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain D: P.177, G.216, K.217 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain E: P.177, G.216, K.217 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain F: P.177, G.216, K.217 Ligand excluded by PLIP

12 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.94, C.173, H.215 Ligands: FMT.2, ZN.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.94, A:C.173, A:H.215, H2O.2 ZN.6: 7 residues within 4Å: Chain A: H.90, H.92, D.94, H.154, C.173 Ligands: FMT.2, ZN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.90, A:H.92, A:H.154, H2O.2 ZN.14: 5 residues within 4Å: Chain B: D.94, C.173, H.215 Ligands: FMT.11, ZN.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.94, B:C.173, B:H.215, H2O.9 ZN.15: 7 residues within 4Å: Chain B: H.90, H.92, D.94, H.154, C.173 Ligands: FMT.11, ZN.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.90, B:H.92, B:H.154, H2O.9 ZN.23: 5 residues within 4Å: Chain C: D.94, C.173, H.215 Ligands: FMT.20, ZN.24 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.94, C:C.173, C:H.215, H2O.17 ZN.24: 7 residues within 4Å: Chain C: H.90, H.92, D.94, H.154, C.173 Ligands: FMT.20, ZN.23 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.90, C:H.92, C:H.154, H2O.17 ZN.32: 5 residues within 4Å: Chain D: D.94, C.173, H.215 Ligands: FMT.29, ZN.33 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.94, D:C.173, D:H.215, H2O.24 ZN.33: 7 residues within 4Å: Chain D: H.90, H.92, D.94, H.154, C.173 Ligands: FMT.29, ZN.32 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.90, D:H.92, D:H.154, H2O.24 ZN.41: 5 residues within 4Å: Chain E: D.94, C.173, H.215 Ligands: FMT.38, ZN.42 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.94, E:C.173, E:H.215, H2O.31 ZN.42: 7 residues within 4Å: Chain E: H.90, H.92, D.94, H.154, C.173 Ligands: FMT.38, ZN.41 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.90, E:H.92, E:H.154, H2O.31 ZN.50: 5 residues within 4Å: Chain F: D.94, C.173, H.215 Ligands: FMT.47, ZN.51 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.94, F:C.173, F:H.215, H2O.38 ZN.51: 7 residues within 4Å: Chain F: H.90, H.92, D.94, H.154, C.173 Ligands: FMT.47, ZN.50 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.90, F:H.92, F:H.154, H2O.38

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: I.136, Y.149, G.151, G.152, E.156, N.190, Y.193 Ligands: GOL.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.149, A:G.152, A:N.190 Water bridges: A:N.190 GOL.8: 3 residues within 4Å: Chain A: Y.55, R.84, E.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.55, A:R.84, A:R.84 GOL.16: 8 residues within 4Å: Chain B: I.136, Y.149, G.151, G.152, E.156, N.190, Y.193 Ligands: GOL.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.149, B:G.152, B:N.190 Water bridges: B:N.190 GOL.17: 3 residues within 4Å: Chain B: Y.55, R.84, E.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.55, B:R.84, B:R.84 GOL.25: 8 residues within 4Å: Chain C: I.136, Y.149, G.151, G.152, E.156, N.190, Y.193 Ligands: GOL.52 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.149, C:G.152, C:N.190 Water bridges: C:N.190 GOL.26: 3 residues within 4Å: Chain C: Y.55, R.84, E.143 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.55, C:R.84, C:R.84 GOL.34: 8 residues within 4Å: Chain D: I.136, Y.149, G.151, G.152, E.156, N.190, Y.193 Ligands: GOL.16 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.149, D:Y.149, D:G.152, D:N.190 Water bridges: D:N.190 GOL.35: 3 residues within 4Å: Chain D: Y.55, R.84, E.143 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.55, D:Y.55, D:R.84, D:R.84 GOL.43: 8 residues within 4Å: Chain E: I.136, Y.149, G.151, G.152, E.156, N.190, Y.193 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.149, E:Y.149, E:G.152, E:N.190 Water bridges: E:N.190 GOL.44: 3 residues within 4Å: Chain E: Y.55, R.84, E.143 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.55, E:Y.55, E:R.84, E:R.84 GOL.52: 8 residues within 4Å: Chain F: I.136, Y.149, G.151, G.152, E.156, N.190, Y.193 Ligands: GOL.25 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.149, F:Y.149, F:G.152, F:N.190 Water bridges: F:N.190 GOL.53: 3 residues within 4Å: Chain F: Y.55, R.84, E.143 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.55, F:Y.55, F:R.84, F:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Metallo Beta Lactamase from Hirschia baltica. To Be Published

Release Date

2019-12-25

Peptides

Beta-lactamase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Beta-lactamase

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