SMTL ID : 3qh8.1

Crystal structure of a beta-lactamase-like protein bound to AMP from brucella melitensis, long wavelength synchrotron data

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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.7: 6 residues within 4Å: Chain B: D.92, H.93, D.190, H.243 Ligands: MN.8, AMP.10 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.8: 6 residues within 4Å: Chain B: H.88, H.90, H.172, D.190 Ligands: MN.7, AMP.10 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.10, 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.254, A:T.257, A:P.258, A:V.261, H2O.10 K.9: 4 residues within 4Å: Chain B: M.254, T.257, P.258, V.261 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:M.254, B:T.257, B:P.258, B:V.261, H2O.22

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 16 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, EDO.5 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.20, A:S.20, A:A.91, B:R.101 Water bridges: A:S.20, A:S.20, B:D.98, B:Y.139 Salt bridges: A:H.90, A:H.172, A:H.221, A:H.243 pi-Cation interactions: A:H.90 pi-Stacking: B:Y.129, B:Y.129, B:Y.139 AMP.10: 16 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.7, MN.8, EDO.11 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.20, B:S.20, B:A.91, 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: H.90, D.174 Chain B: S.137, Y.139 Ligands: AMP.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.174 Water bridges: A:P.89, A:D.174, B:Y.139 EDO.11: 5 residues within 4Å: Chain A: S.137, Y.139 Chain B: H.90, D.174 Ligands: AMP.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.174 Water bridges: B:P.89, B:D.174, A:Y.139

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

TLA.6: 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.12: 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., Crystal structure of a Beta-Lactamase-Like Protein bound to AMP from Brucella Melitensis, long wavelength synchrotron data. Acta Crystallogr.,Sect.F (2011)

Release Date

2011-02-09

Peptides

Beta-lactamase-like: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-lactamase-like

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