SMTL ID : 4kjm.1 (1 other biounit)

Crystal structure of the Staphylococcus aureus protein (NP_646141.1, domain 3912-4037) similar to streptococcal adhesins emb and ebhA/ebhB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: H.70, L.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.22, A:L.72 NA.22: 2 residues within 4Å: Chain B: H.70, L.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.22, B:L.72

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: S.20, Q.21, N.22 Chain B: D.13 Ligands: ZN.15, ZN.16 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: H.121 Ligands: ZN.17 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain A: D.13 Chain B: S.20, Q.21, N.22 Ligands: ZN.3, ZN.4 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: N.12 Chain B: L.78, Q.111 Ligand excluded by PLIP

18 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: D.13 Ligands: ZN.4, CL.21 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.13, H2O.5, H2O.5, H2O.10, H2O.11 ZN.4: 4 residues within 4Å: Chain A: D.13, K.69 Ligands: ZN.3, CL.21 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.13, H2O.5, H2O.5, H2O.5 ZN.5: 1 residues within 4Å: Chain A: D.118 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.118, A:D.118, H2O.6, H2O.6, H2O.6 ZN.6: 2 residues within 4Å: Chain A: H.121, E.125 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.121, A:E.125, H2O.5, H2O.6, H2O.6 ZN.7: 1 residues within 4Å: Chain A: H.121 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.121, H2O.5, H2O.6, H2O.6, H2O.6 ZN.8: 1 residues within 4Å: Chain A: H.70 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.70, H2O.6, H2O.6, H2O.6 ZN.9: 1 residues within 4Å: Chain A: E.125 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.125, A:E.125, H2O.6, H2O.6, H2O.6 ZN.10: 1 residues within 4Å: Chain B: N.108 No protein-ligand interaction detected (PLIP) ZN.11: 1 residues within 4Å: Chain A: D.94 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.94, A:D.94, H2O.6, H2O.6 ZN.14: 1 residues within 4Å: Chain B: D.27 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.27, B:D.27, H2O.11, H2O.11, H2O.11 ZN.15: 3 residues within 4Å: Chain B: D.13 Ligands: CL.2, ZN.16 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.13, B:D.13, H2O.4, H2O.11, H2O.11 ZN.16: 4 residues within 4Å: Chain B: D.13, K.69 Ligands: CL.2, ZN.15 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.13, H2O.11, H2O.11 ZN.17: 2 residues within 4Å: Chain B: H.121 Ligands: CL.13 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.121, H2O.11 ZN.18: 2 residues within 4Å: Chain B: H.121, E.125 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.121, B:E.125, H2O.9, H2O.11, H2O.11 ZN.19: 1 residues within 4Å: Chain B: E.125 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.125, H2O.9, H2O.11, H2O.11, H2O.11 ZN.20: 1 residues within 4Å: Chain B: D.118 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.118, H2O.11, H2O.11, H2O.11, H2O.11 ZN.23: 1 residues within 4Å: Chain B: H.70 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.70, H2O.10, H2O.10, H2O.12, H2O.12 ZN.25: 1 residues within 4Å: Chain B: E.59 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.59, H2O.11, H2O.12, H2O.12, H2O.12

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

ACT.12: 2 residues within 4Å: Chain B: L.24, R.112 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.24 Salt bridges: B:R.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cymborowski, M. et al., Crystal structure of the Staphylococcus aureus protein (NP_646141.1, domain 3912-4037) similar to streptococcal adhesins emb and ebhA/ebhB. To be Published

Release Date

2013-05-29

Peptides

Extracellular matrix-binding protein ebh: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Extracellular matrix-binding protein ebh

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