SMTL ID : 2y4y.1

Structure of a domain from the type IV pilus biogenesis lipoprotein PilP, from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-octamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.47 Chain C: E.25 Ligands: ACT.5 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:E.25, A:H.47, ACT.5, H2O.84 ZN.4: 1 residues within 4Å: Chain A: E.85 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.85, A:E.85, H2O.86, H2O.87 ZN.6: 3 residues within 4Å: Chain B: H.47 Chain F: H.47 Ligands: ZN.18 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: F:H.47, B:H.47, H2O.157, H2O.456 ZN.7: 1 residues within 4Å: Chain B: E.85 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.85, H2O.158 ZN.8: 2 residues within 4Å: Chain B: E.25 Chain C: H.47 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.47, B:E.25, B:E.25, H2O.234, H2O.235 ZN.12: 2 residues within 4Å: Chain A: E.25 Chain D: H.47 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:E.25, A:E.25, D:H.47, H2O.296, H2O.298 ZN.13: 3 residues within 4Å: Chain E: H.47 Chain G: E.25 Ligands: ACT.17 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: E:H.47, G:E.25, H2O.383 ZN.16: 1 residues within 4Å: Chain E: E.85 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.85, E:E.85, H2O.385, H2O.386 ZN.18: 3 residues within 4Å: Chain B: H.47 Chain F: H.47 Ligands: ZN.6 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: F:H.47, B:H.47, H2O.157, H2O.456 ZN.19: 1 residues within 4Å: Chain F: E.85 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.85, H2O.457 ZN.20: 2 residues within 4Å: Chain F: E.25 Chain G: H.47 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: G:H.47, F:E.25, F:E.25, H2O.533, H2O.534 ZN.24: 2 residues within 4Å: Chain E: E.25 Chain H: H.47 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: E:E.25, E:E.25, H:H.47, H2O.595, H2O.597

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

ACT.2: 4 residues within 4Å: Chain A: N.32, R.48 Chain G: V.27 Ligands: ACT.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.32 Hydrogen bonds: A:N.32 Salt bridges: A:R.48 ACT.3: 4 residues within 4Å: Chain A: L.39, V.46, R.48 Ligands: ACT.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.46 Salt bridges: A:R.48 ACT.5: 5 residues within 4Å: Chain A: H.47, R.48 Chain C: E.25, V.27 Ligands: ZN.1 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.27 Water bridges: C:K.41, C:K.93, C:K.93 Salt bridges: C:K.41, C:K.93, A:H.47 Hydrogen bonds: A:R.48 ACT.9: 3 residues within 4Å: Chain C: N.32, R.48 Chain E: V.27 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:V.27 Hydrogen bonds: C:N.32 Salt bridges: C:R.48 ACT.10: 4 residues within 4Å: Chain C: L.39, R.48 Ligands: ACT.14, ACT.15 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.48 ACT.11: 5 residues within 4Å: Chain D: L.30, N.32, R.48 Chain F: V.27, L.39 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:V.27, F:L.39 Hydrogen bonds: D:N.32 Salt bridges: D:R.48 ACT.14: 4 residues within 4Å: Chain C: V.27 Chain E: N.32, R.48 Ligands: ACT.10 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:N.32 Hydrogen bonds: E:N.32 Salt bridges: E:R.48 ACT.15: 4 residues within 4Å: Chain E: L.39, V.46, R.48 Ligands: ACT.10 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.46 Salt bridges: E:R.48 ACT.17: 5 residues within 4Å: Chain E: H.47, R.48 Chain G: E.25, V.27 Ligands: ZN.13 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain G Hydrogen bonds: E:R.48 Water bridges: E:V.46, G:K.41, G:K.93, G:K.93 Salt bridges: E:H.47, G:K.41, G:K.93 Hydrophobic interactions: G:V.27 ACT.21: 3 residues within 4Å: Chain A: V.27 Chain G: N.32, R.48 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:V.27 Hydrogen bonds: G:N.32 Salt bridges: G:R.48 ACT.22: 4 residues within 4Å: Chain G: L.39, R.48 Ligands: ACT.2, ACT.3 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.48 ACT.23: 5 residues within 4Å: Chain B: V.27, L.39 Chain H: L.30, N.32, R.48 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: B:V.27, B:L.39 Hydrogen bonds: H:N.32 Salt bridges: H:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berry, J. et al., Structure of a Domain from the Type Iv Pilus Biogenesis Lipoprotein Pilp, from Pseudomonas Aeruginosa. To be Published

Release Date

2012-01-18

Peptides

PILP PROTEIN: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

PILP PROTEIN

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