SMTL ID : 3lnl.1

Crystal structure of Staphylococcus aureus protein SA1388

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.68, D.106, E.333 Ligands: ZN.2, B3P.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.68, A:D.106, A:E.333, H2O.13, H2O.13 ZN.2: 5 residues within 4Å: Chain A: H.69, H.330, E.333 Ligands: ZN.1, B3P.3 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.69, A:H.330, A:E.333, H2O.13, H2O.13, H2O.17 ZN.4: 5 residues within 4Å: Chain B: H.69, H.330, E.333 Ligands: ZN.5, B3P.6 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.69, B:H.330, B:E.333, H2O.11, H2O.26, H2O.27 ZN.5: 5 residues within 4Å: Chain B: H.68, D.106, E.333 Ligands: ZN.4, B3P.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.68, B:D.106, B:E.333, H2O.26, H2O.27 ZN.7: 5 residues within 4Å: Chain C: H.68, D.106, E.333 Ligands: ZN.8, B3P.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.68, C:D.106, C:E.333, H2O.39, H2O.39 ZN.8: 5 residues within 4Å: Chain C: H.69, H.330, E.333 Ligands: ZN.7, B3P.9 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.69, C:H.330, C:E.333, H2O.39, H2O.40, H2O.44 ZN.10: 5 residues within 4Å: Chain D: H.69, H.330, E.333 Ligands: ZN.11, B3P.12 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.69, D:H.330, D:E.333, H2O.38, H2O.52, H2O.53 ZN.11: 5 residues within 4Å: Chain D: H.68, D.106, E.333 Ligands: ZN.10, B3P.12 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.68, D:D.106, D:E.333, H2O.52, H2O.53 ZN.13: 5 residues within 4Å: Chain E: H.68, D.106, E.333 Ligands: ZN.14, B3P.15 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.68, E:D.106, E:E.333, H2O.66, H2O.66 ZN.14: 5 residues within 4Å: Chain E: H.69, H.330, E.333 Ligands: ZN.13, B3P.15 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.69, E:H.330, E:E.333, H2O.66, H2O.66, H2O.71 ZN.16: 5 residues within 4Å: Chain F: H.69, H.330, E.333 Ligands: ZN.17, B3P.18 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.69, F:H.330, F:E.333, H2O.65, H2O.79, H2O.80 ZN.17: 5 residues within 4Å: Chain F: H.68, D.106, E.333 Ligands: ZN.16, B3P.18 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.68, F:D.106, F:E.333, H2O.79, H2O.80

6 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.3: 12 residues within 4Å: Chain A: W.26, F.73, H.102, T.103, D.106, L.242, I.286, G.287, G.288, S.289 Ligands: ZN.1, ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.26, A:H.102, A:G.287, A:S.289, A:S.289 B3P.6: 11 residues within 4Å: Chain B: W.26, F.73, H.102, T.103, D.106, L.242, G.287, G.288, S.289 Ligands: ZN.4, ZN.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.26, B:H.102, B:G.287, B:S.289, B:S.289 B3P.9: 12 residues within 4Å: Chain C: W.26, F.73, H.102, T.103, D.106, L.242, I.286, G.287, G.288, S.289 Ligands: ZN.7, ZN.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.26, C:H.102, C:G.287, C:S.289, C:S.289 B3P.12: 11 residues within 4Å: Chain D: W.26, F.73, H.102, T.103, D.106, L.242, G.287, G.288, S.289 Ligands: ZN.10, ZN.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:W.26, D:H.102, D:G.287, D:S.289, D:S.289 B3P.15: 12 residues within 4Å: Chain E: W.26, F.73, H.102, T.103, D.106, L.242, I.286, G.287, G.288, S.289 Ligands: ZN.13, ZN.14 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:W.26, E:H.102, E:G.287, E:S.289, E:S.289 B3P.18: 11 residues within 4Å: Chain F: W.26, F.73, H.102, T.103, D.106, L.242, G.287, G.288, S.289 Ligands: ZN.16, ZN.17 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:W.26, F:H.102, F:G.287, F:S.289, F:S.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh Saikatendu, K. et al., Structure of a Conserved Hypothetical Protein Sa1388 from S. aureus Reveals a Capped Hexameric Toroid with Two Pii Domain Lids and a Dinuclear Metal Center. Bmc Struct.Biol. (2006)

Release Date

2010-03-16

Peptides

UPF0135 protein SA1388: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

UPF0135 protein SA1388