SMTL ID : 3py5.1

Crystal structure of a beta-lactamase-like protein from brucella melitensis bound to AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.92, H.93, D.190, H.243 Ligands: MN.2, AMP.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.92, A:H.93, A:D.190, A:H.243, H2O.2 MN.2: 6 residues within 4Å: Chain A: H.88, H.90, H.172, D.190 Ligands: MN.1, AMP.4 6 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.88, A:H.90, A:H.172, A:D.190, H2O.2, AMP.4 MN.6: 6 residues within 4Å: Chain B: D.92, H.93, D.190, H.243 Ligands: MN.7, AMP.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.92, B:H.93, B:D.190, B:H.243, H2O.14 MN.7: 6 residues within 4Å: Chain B: H.88, H.90, H.172, D.190 Ligands: MN.6, AMP.9 6 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.88, B:H.90, B:H.172, B:D.190, AMP.9, H2O.14

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: M.254, T.257, P.258, V.261 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:M.254, A:T.257, A:T.257, A:P.258, A:V.261 K.8: 4 residues within 4Å: Chain B: M.254, T.257, P.258, V.261 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:M.254, B:T.257, B:T.257, B:P.258, B:V.261

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 15 residues within 4Å: Chain A: S.20, P.89, H.90, A.91, D.92, H.172, D.190, H.221, H.243 Chain B: D.98, R.101, Y.129, Y.139 Ligands: MN.1, MN.2 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:R.101, B:Y.139, A:S.20, A:S.20, A:A.91 Water bridges: B:D.98, A:S.20, A:S.20 pi-Stacking: B:Y.129, B:Y.129, B:Y.139 Salt bridges: A:H.90, A:H.172, A:H.221, A:H.243 pi-Cation interactions: A:H.90 AMP.9: 15 residues within 4Å: Chain A: D.98, R.101, Y.129, Y.139 Chain B: S.20, P.89, H.90, A.91, D.92, H.172, D.190, H.221, H.243 Ligands: MN.6, MN.7 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.20, B:S.20, B:A.91, A:R.101, A:R.101, A:Y.139 Water bridges: B:S.20, B:S.20 Salt bridges: B:H.90, B:H.172, B:H.221, B:H.243 pi-Cation interactions: B:H.90 pi-Stacking: A:Y.129, A:Y.129, A:Y.139

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.5: 4 residues within 4Å: Chain A: R.25, Q.214, H.218, H.245 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Water bridges: A:R.25, A:R.25, A:H.245 Salt bridges: A:R.25, A:H.218, A:H.245 TLA.10: 4 residues within 4Å: Chain B: R.25, Q.214, H.218, H.245 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.214, B:Q.214 Water bridges: B:R.25, B:R.25, B:H.245 Salt bridges: B:R.25, B:H.218, B:H.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., BrabA.11339.a: anomalous diffraction and ligand binding guide towards the elucidation of the function of a `putative beta-lactamase-like protein from Brucella melitensis. Acta Crystallogr.,Sect.F (2011)

Release Date

2010-12-29

Peptides

Beta-lactamase-like: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-lactamase-like

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