SMTL ID : 4nt9.1 (3 other biounits)

Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.134, D.141, E.185, H.188 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.134, A:D.141, A:E.185, A:H.188, H2O.1, H2O.1 ZN.4: 4 residues within 4Å: Chain B: H.134, D.141, E.185, H.188 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.134, B:D.141, B:E.185, B:H.188, H2O.6, H2O.7 ZN.8: 4 residues within 4Å: Chain C: H.134, D.141, E.185, H.188 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.134, C:D.141, C:E.185, C:H.188, H2O.11, H2O.11

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 9 residues within 4Å: Chain A: R.101, Q.106, Y.125, S.126, A.127, S.132, H.134, E.185 Ligands: GOL.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.127 Hydrogen bonds: A:Q.106 Water bridges: A:R.101, A:S.132, A:E.133 Salt bridges: A:R.101, A:H.134 ACT.5: 7 residues within 4Å: Chain B: R.101, Q.106, S.126, A.127, S.132, H.134, E.185 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.127 Hydrogen bonds: B:Q.106, B:S.126, B:A.127, B:S.132 Water bridges: B:R.101, B:R.101, B:E.133 Salt bridges: B:R.101, B:H.134 ACT.9: 8 residues within 4Å: Chain C: R.101, Q.106, Y.125, S.126, A.127, S.132, H.134, E.185 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.127 Hydrogen bonds: C:Q.106, C:S.126, C:S.132 Water bridges: C:R.101, C:E.133 Salt bridges: C:R.101, C:H.134

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: L.109, Y.113, Y.125, S.126, E.185, W.187 Ligands: ACT.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.101, A:S.126, A:W.187 Water bridges: A:R.101, A:R.101 GOL.6: 2 residues within 4Å: Chain B: H.96, Y.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.97, B:Y.97 Water bridges: B:E.71, B:K.76 GOL.7: 7 residues within 4Å: Chain A: A.85, Y.166 Chain B: K.59, H.60, Y.131, Y.217, V.218 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.218, A:Y.166 GOL.10: 3 residues within 4Å: Chain C: A.85, E.88, Y.166 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y.H. et al., Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia. To be Published

Release Date

2014-11-12

Peptides

Putative uncharacterized protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Putative uncharacterized protein

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