SMTL ID : 3ocm.3 (2 other biounits)

The crystal structure of a domain from a possible membrane protein of Bordetella parapertussis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 4 residues within 4Å: Chain A: E.153, D.161, E.164 Ligands: ADP.5 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.164, H2O.5, H2O.5, H2O.5, H2O.5, H2O.5 MG.2: 1 residues within 4Å: Chain A: H.69 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:H.69, H2O.4, H2O.5, H2O.5, H2O.5, H2O.5 MG.3: 1 residues within 4Å: Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: I.41, E.153 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.153, H2O.6, H2O.6, H2O.6, H2O.6 MG.9: 1 residues within 4Å: Chain B: H.69 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:H.69, H2O.10, H2O.11, H2O.11, H2O.11, H2O.12 MG.10: 3 residues within 4Å: Chain B: E.153, D.161, E.164 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.164, H2O.11, H2O.11, H2O.11, H2O.11, H2O.11 MG.11: 1 residues within 4Å: Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 15 residues within 4Å: Chain A: T.43, D.47, V.48, S.49, H.69, S.70, F.71, P.73, L.145, T.147, I.149, D.150, D.161 Ligands: MG.1, MG.11 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.43, A:S.49, A:S.49, A:P.68, A:H.69, A:S.70, A:S.70, A:D.150 Water bridges: A:F.71, A:D.150, A:D.150, A:D.150, A:E.153, A:D.161, A:D.161, B:S.70 Salt bridges: A:H.69 pi-Stacking: A:H.69, A:H.69 ADP.12: 15 residues within 4Å: Chain B: T.43, D.47, V.48, S.49, H.69, S.70, F.71, P.73, L.132, L.145, T.147, I.149, D.150, D.161 Ligands: MG.3 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.43, B:S.49, B:S.49, B:S.70, B:T.147, B:D.150 Water bridges: B:F.71, B:D.150, B:E.153, B:E.164, A:S.70 Salt bridges: B:H.69 pi-Stacking: B:H.69, B:H.69

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: R.100, R.102, R.103, N.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.103, A:N.104 Salt bridges: A:R.100, A:R.102 SO4.7: 2 residues within 4Å: Chain A: R.76, R.103 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.76, A:R.103 SO4.8: 1 residues within 4Å: Chain A: R.45 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.45, A:R.45, A:R.45 Salt bridges: A:R.45 SO4.13: 1 residues within 4Å: Chain B: R.45 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.45 Salt bridges: B:R.45 SO4.14: 5 residues within 4Å: Chain B: R.100, V.101, R.102, R.103, N.104 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.103, B:R.103, B:N.104, B:N.104 Salt bridges: B:R.100 SO4.15: 2 residues within 4Å: Chain B: S.37, R.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.37 Water bridges: B:S.37, B:S.37 SO4.16: 3 residues within 4Å: Chain B: S.49, Q.63, A.67 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.63 Water bridges: B:W.50, B:W.50, B:Q.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The crystal structure of a domain from a possible membrane protein of Bordetella parapertussis. To be Published

Release Date

2010-10-06

Peptides

Putative membrane protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative membrane protein

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