SMTL ID : 8vdk.1

Crystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein MSCRAMM_SdrD from Staphylococcus aureus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: D.56, T.90, N.93, D.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.90, A:N.93, A:N.93 GOL.2: 4 residues within 4Å: Chain A: Y.208, M.295, G.309, A.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.208, A:G.309 Water bridges: A:A.311 GOL.7: 3 residues within 4Å: Chain A: N.360, N.363, R.388 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.363, A:N.363, A:R.388 Water bridges: A:N.360, A:N.360

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: I.420, T.421, N.427, S.429 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.421, A:T.421, A:T.421, A:N.427, A:N.427, A:S.429 EDO.4: 4 residues within 4Å: Chain A: Q.59, D.120, D.122, D.238 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.120, A:D.120, A:A.121, A:D.122 EDO.5: 3 residues within 4Å: Chain A: V.16, I.25, A.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.145 Water bridges: A:V.16 EDO.6: 3 residues within 4Å: Chain A: I.141, T.142, T.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.141, A:T.143 EDO.8: 4 residues within 4Å: Chain A: T.39, V.40, D.41, D.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.41, A:D.42 Water bridges: A:V.40, A:V.40 EDO.9: 5 residues within 4Å: Chain A: Y.102, F.106, N.107, S.108, V.109 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.107 Water bridges: A:D.76, A:N.79, A:D.374, A:D.374, A:D.374, A:D.374 EDO.10: 3 residues within 4Å: Chain A: Y.31, S.116, Y.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.116 EDO.11: 7 residues within 4Å: Chain A: E.81, N.331, E.410, L.428, S.429, D.431 Ligands: CA.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.81, A:N.331 Water bridges: A:Q.343

5 x CA: CALCIUM ION(Non-covalent)

CA.12: 3 residues within 4Å: Chain A: D.42, V.44, V.103 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.42, A:V.44, H2O.2, H2O.11, H2O.11 CA.13: 6 residues within 4Å: Chain A: D.336, N.338, N.340, V.342, E.344, E.347 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.336, A:V.342, A:E.344, A:E.347, A:E.347 CA.14: 4 residues within 4Å: Chain A: E.409, D.412, N.414, S.429 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.409, A:D.412, A:S.429, H2O.4, H2O.6 CA.15: 5 residues within 4Å: Chain A: D.18, D.20, S.22, T.24, D.30 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.18, A:S.22, A:T.24, A:D.30, A:D.30 CA.16: 4 residues within 4Å: Chain A: N.331, L.428, D.431 Ligands: EDO.11 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.428, A:D.431, A:D.431, H2O.1, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein MSCRAMM_SdrD from Staphylococcus aureus. To Be Published

Release Date

2024-08-07

Peptides

Serine-aspartate repeat-containing protein D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serine-aspartate repeat-containing protein D