SMTL ID : 3ocm.1 (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-octamer

Ligands

28 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) MG.17: 4 residues within 4Å: Chain C: E.153, D.161, E.164 Ligands: ADP.21 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.164, H2O.17, H2O.17, H2O.17, H2O.17, H2O.17 MG.18: 1 residues within 4Å: Chain C: H.69 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:H.69, H2O.17, H2O.17, H2O.17, H2O.17, H2O.17 MG.19: 1 residues within 4Å: Ligands: ADP.28 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain C: I.41, E.153 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.153, H2O.18, H2O.18, H2O.18, H2O.18 MG.25: 1 residues within 4Å: Chain D: H.69 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:H.69, H2O.23, H2O.23, H2O.23, H2O.23, H2O.24 MG.26: 3 residues within 4Å: Chain D: E.153, D.161, E.164 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.164, H2O.23, H2O.23, H2O.23, H2O.23, H2O.24 MG.27: 1 residues within 4Å: Ligands: ADP.21 No protein-ligand interaction detected (PLIP) MG.33: 4 residues within 4Å: Chain E: E.153, D.161, E.164 Ligands: ADP.37 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:E.164, H2O.29, H2O.29, H2O.29, H2O.29, H2O.29 MG.34: 1 residues within 4Å: Chain E: H.69 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:H.69, H2O.29, H2O.29, H2O.29, H2O.29, H2O.30 MG.35: 1 residues within 4Å: Ligands: ADP.44 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain E: I.41, E.153 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.153, H2O.30, H2O.30, H2O.31, H2O.31 MG.41: 1 residues within 4Å: Chain F: H.69 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:H.69, H2O.35, H2O.35, H2O.35, H2O.35, H2O.36 MG.42: 3 residues within 4Å: Chain F: E.153, D.161, E.164 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.164, H2O.35, H2O.35, H2O.36, H2O.36, H2O.36 MG.43: 1 residues within 4Å: Ligands: ADP.37 No protein-ligand interaction detected (PLIP) MG.49: 4 residues within 4Å: Chain G: E.153, D.161, E.164 Ligands: ADP.53 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:E.164, H2O.41, H2O.41, H2O.42, H2O.42, H2O.42 MG.50: 1 residues within 4Å: Chain G: H.69 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:H.69, H2O.41, H2O.41, H2O.41, H2O.42, H2O.42 MG.51: 1 residues within 4Å: Ligands: ADP.60 No protein-ligand interaction detected (PLIP) MG.52: 2 residues within 4Å: Chain G: I.41, E.153 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:E.153, H2O.43, H2O.43, H2O.43, H2O.43 MG.57: 1 residues within 4Å: Chain H: H.69 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:H.69, H2O.47, H2O.47, H2O.47, H2O.48, H2O.48 MG.58: 3 residues within 4Å: Chain H: E.153, D.161, E.164 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.164, H2O.47, H2O.48, H2O.48, H2O.48, H2O.48 MG.59: 1 residues within 4Å: Ligands: ADP.53 No protein-ligand interaction detected (PLIP)

8 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 ADP.21: 15 residues within 4Å: Chain C: 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.17, MG.27 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.43, C:S.49, C:S.49, C:P.68, C:H.69, C:S.70, C:S.70, C:D.150 Water bridges: C:F.71, C:D.150, C:D.150, C:D.150, C:E.153, C:D.161, C:D.161, D:S.70 Salt bridges: C:H.69 pi-Stacking: C:H.69, C:H.69 ADP.28: 15 residues within 4Å: Chain D: 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.19 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.43, D:S.49, D:S.49, D:S.70, D:T.147, D:D.150 Water bridges: D:P.68, D:F.71, D:D.150, D:E.153, D:E.164, C:S.70 Salt bridges: D:H.69 pi-Stacking: D:H.69, D:H.69 ADP.37: 15 residues within 4Å: Chain E: 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.33, MG.43 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.43, E:S.49, E:S.49, E:P.68, E:H.69, E:S.70, E:S.70, E:D.150 Water bridges: E:F.71, E:D.150, E:D.150, E:D.150, E:E.153, E:D.161, E:D.161, F:S.70 Salt bridges: E:H.69 pi-Stacking: E:H.69, E:H.69 ADP.44: 15 residues within 4Å: Chain F: 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.35 14 PLIP interactions: 13 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:T.43, F:S.49, F:S.49, F:S.70, F:T.147, F:D.150 Water bridges: F:F.71, F:D.150, F:E.153, F:E.164, E:S.70 Salt bridges: F:H.69 pi-Stacking: F:H.69, F:H.69 ADP.53: 15 residues within 4Å: Chain G: 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.49, MG.59 19 PLIP interactions: 18 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:T.43, G:S.49, G:S.49, G:P.68, G:H.69, G:S.70, G:S.70, G:D.150 Water bridges: G:F.71, G:D.150, G:D.150, G:D.150, G:E.153, G:D.161, G:E.164, H:S.70 Salt bridges: G:H.69 pi-Stacking: G:H.69, G:H.69 ADP.60: 15 residues within 4Å: Chain H: 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.51 15 PLIP interactions: 14 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:T.43, H:S.49, H:S.49, H:S.70, H:T.147, H:D.150 Water bridges: H:P.68, H:F.71, H:D.150, H:E.153, H:E.164, G:S.70 Salt bridges: H:H.69 pi-Stacking: H:H.69, H:H.69

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

SO4.6: 5 residues within 4Å: Chain A: R.100, R.102, R.103, N.104 Ligands: SO4.40 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: R.76, R.103 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: R.45 Chain G: N.104 Ligands: SO4.54 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain B: R.45 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: R.100, V.101, R.102, R.103, N.104 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: S.37, R.39 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: S.49, Q.63, A.67 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain C: R.100, R.102, R.103, N.104 Ligands: SO4.56 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain C: R.76, R.103 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain C: R.45 Chain E: N.104 Ligands: SO4.38 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain D: R.45 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain D: R.100, V.101, R.102, R.103, N.104 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain D: S.37, R.39 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain D: S.49, Q.63, A.67 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain E: R.100, R.102, R.103, N.104 Ligands: SO4.24 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain E: R.76, R.103 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain A: N.104 Chain E: R.45 Ligands: SO4.6 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Chain F: R.45 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain F: R.100, V.101, R.102, R.103, N.104 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain F: S.37, R.39 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain F: S.49, Q.63, A.67 Ligand excluded by PLIP SO4.54: 5 residues within 4Å: Chain G: R.100, R.102, R.103, N.104 Ligands: SO4.8 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain G: R.76, R.103 Ligand excluded by PLIP SO4.56: 3 residues within 4Å: Chain C: N.104 Chain G: R.45 Ligands: SO4.22 Ligand excluded by PLIP SO4.61: 1 residues within 4Å: Chain H: R.45 Ligand excluded by PLIP SO4.62: 5 residues within 4Å: Chain H: R.100, V.101, R.102, R.103, N.104 Ligand excluded by PLIP SO4.63: 2 residues within 4Å: Chain H: S.37, R.39 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain H: S.49, Q.63, A.67 Ligand excluded by PLIP

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Putative membrane protein

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