SMTL ID : 6v71.1

Crystal Structure of Metallo Beta Lactamase from Hirschia baltica with Nitrate in the Active Site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-trimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.94, C.173, H.215 Ligands: ZN.2, NO3.4 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.2: 6 residues within 4Å: Chain A: H.90, H.92, D.94, H.154 Ligands: ZN.1, NO3.4 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.20: 5 residues within 4Å: Chain B: D.94, C.173, H.215 Ligands: ZN.21, NO3.23 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.94, B:C.173, B:H.215, H2O.8 ZN.21: 6 residues within 4Å: Chain B: H.90, H.92, D.94, H.154 Ligands: ZN.20, NO3.23 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.90, B:H.92, B:H.154, H2O.8 ZN.39: 5 residues within 4Å: Chain C: D.94, C.173, H.215 Ligands: ZN.40, NO3.42 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.94, C:C.173, C:H.215, H2O.14 ZN.40: 6 residues within 4Å: Chain C: H.90, H.92, D.94, H.154 Ligands: ZN.39, NO3.42 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.90, C:H.92, C:H.154, H2O.14

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

EDO.3: 9 residues within 4Å: Chain A: T.112, L.114, T.115, I.133, S.134, Y.149, D.157, I.159 Ligands: NO3.8 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: A.189, N.190, L.191, G.192 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: V.36, P.38, P.39, W.40, G.41 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: T.26, G.27, I.50, E.51, E.163, V.165 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain C: D.65, A.66, A.69, A.101 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: K.23, L.24, G.25, T.26 Ligands: NO3.5 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: Q.209, G.220, R.221 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain B: T.112, L.114, T.115, I.133, S.134, Y.149, D.157, I.159 Ligands: NO3.27 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: A.189, N.190, L.191, G.192 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: V.36, P.38, P.39, W.40, G.41 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: T.26, G.27, I.50, E.51, E.163, V.165 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain A: D.65, A.66, A.69, A.101 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: K.23, L.24, G.25, T.26 Ligands: NO3.24 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: Q.209, G.220, R.221 Ligand excluded by PLIP EDO.41: 9 residues within 4Å: Chain C: T.112, L.114, T.115, I.133, S.134, Y.149, D.157, I.159 Ligands: NO3.46 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain C: A.189, N.190, L.191, G.192 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain C: V.36, P.38, P.39, W.40, G.41 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain C: T.26, G.27, I.50, E.51, E.163, V.165 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain B: D.65, A.66, A.69, A.101 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain C: K.23, L.24, G.25, T.26 Ligands: NO3.43 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain C: Q.209, G.220, R.221 Ligand excluded by PLIP

24 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 9 residues within 4Å: Chain A: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.1, ZN.2, NO3.9 Ligand excluded by PLIP NO3.5: 3 residues within 4Å: Chain A: K.23, T.26 Ligands: EDO.15 Ligand excluded by PLIP NO3.6: 3 residues within 4Å: Chain A: N.64, D.65, G.97 Ligand excluded by PLIP NO3.8: 8 residues within 4Å: Chain A: T.112, D.113, L.114, L.131, N.132, I.133, S.134 Ligands: EDO.3 Ligand excluded by PLIP NO3.9: 6 residues within 4Å: Chain A: I.43, R.176, P.177, G.184, H.215 Ligands: NO3.4 Ligand excluded by PLIP NO3.10: 3 residues within 4Å: Chain A: K.35, W.63, N.64 Ligand excluded by PLIP NO3.11: 5 residues within 4Å: Chain A: Y.34, N.42, I.43, R.44, H.215 Ligand excluded by PLIP NO3.18: 3 residues within 4Å: Chain A: S.182, L.183, G.184 Ligand excluded by PLIP NO3.23: 9 residues within 4Å: Chain B: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.20, ZN.21, NO3.28 Ligand excluded by PLIP NO3.24: 3 residues within 4Å: Chain B: K.23, T.26 Ligands: EDO.34 Ligand excluded by PLIP NO3.25: 3 residues within 4Å: Chain B: N.64, D.65, G.97 Ligand excluded by PLIP NO3.27: 8 residues within 4Å: Chain B: T.112, D.113, L.114, L.131, N.132, I.133, S.134 Ligands: EDO.22 Ligand excluded by PLIP NO3.28: 6 residues within 4Å: Chain B: I.43, R.176, P.177, G.184, H.215 Ligands: NO3.23 Ligand excluded by PLIP NO3.29: 3 residues within 4Å: Chain B: K.35, W.63, N.64 Ligand excluded by PLIP NO3.30: 5 residues within 4Å: Chain B: Y.34, N.42, I.43, R.44, H.215 Ligand excluded by PLIP NO3.37: 3 residues within 4Å: Chain B: S.182, L.183, G.184 Ligand excluded by PLIP NO3.42: 9 residues within 4Å: Chain C: H.154, C.173, R.176, G.184, N.185, H.215 Ligands: ZN.39, ZN.40, NO3.47 Ligand excluded by PLIP NO3.43: 3 residues within 4Å: Chain C: K.23, T.26 Ligands: EDO.53 Ligand excluded by PLIP NO3.44: 3 residues within 4Å: Chain C: N.64, D.65, G.97 Ligand excluded by PLIP NO3.46: 8 residues within 4Å: Chain C: T.112, D.113, L.114, L.131, N.132, I.133, S.134 Ligands: EDO.41 Ligand excluded by PLIP NO3.47: 6 residues within 4Å: Chain C: I.43, R.176, P.177, G.184, H.215 Ligands: NO3.42 Ligand excluded by PLIP NO3.48: 3 residues within 4Å: Chain C: K.35, W.63, N.64 Ligand excluded by PLIP NO3.49: 5 residues within 4Å: Chain C: Y.34, N.42, I.43, R.44, H.215 Ligand excluded by PLIP NO3.56: 3 residues within 4Å: Chain C: S.182, L.183, G.184 Ligand excluded by PLIP

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

FMT.17: 4 residues within 4Å: Chain A: M.30, R.44, K.217, P.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.44, A:R.44 FMT.36: 4 residues within 4Å: Chain B: M.30, R.44, K.217, P.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.44, B:R.44 FMT.55: 4 residues within 4Å: Chain C: M.30, R.44, K.217, P.218 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.44, C:R.44

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.19: 5 residues within 4Å: Chain A: K.128 Chain B: K.128 Chain C: K.128 Ligands: PO4.38, PO4.57 9 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:K.128 Water bridges: B:E.108, B:K.128, C:E.108, A:E.108, A:E.108 Salt bridges: B:K.128, C:K.128, A:K.128 PO4.38: 5 residues within 4Å: Chain A: K.128 Chain B: K.128 Chain C: K.128 Ligands: PO4.19, PO4.57 9 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, 4 interactions with chain A Water bridges: B:E.108, C:E.108, A:E.108, A:E.108, A:K.128 Salt bridges: B:K.128, C:K.128, A:K.128 Hydrogen bonds: C:K.128 PO4.57: 5 residues within 4Å: Chain A: K.128 Chain B: K.128 Chain C: K.128 Ligands: PO4.19, PO4.38 9 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 4 interactions with chain A Water bridges: B:E.108, B:K.128, C:E.108, A:E.108, A:K.128 Salt bridges: B:K.128, C:K.128, A:K.128 Hydrogen bonds: A:K.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Metallo Beta Lactamase from Hirschia baltica with Nitrate in the Active Site. To Be Published

Release Date

2019-12-25

Peptides

Beta-lactamase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Beta-lactamase

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