SMTL ID : 4jpd.1

The structure of CyaY from Burkholderia cenocepacia

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: H.33, D.34, I.35, F.48, E.49, A.104 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.33, A:I.35 Hydrogen bonds: A:D.34, A:D.34, A:E.49 Water bridges: A:N.50 ACT.2: 3 residues within 4Å: Chain A: H.75, T.86, R.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.86 Salt bridges: A:H.75 ACT.5: 6 residues within 4Å: Chain B: H.33, D.34, I.35, F.48, E.49, A.104 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.33, B:I.35 Hydrogen bonds: B:D.34, B:D.34, B:E.49 Water bridges: B:N.50 ACT.6: 3 residues within 4Å: Chain B: H.75, T.86, R.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.86 Salt bridges: B:H.75 ACT.9: 6 residues within 4Å: Chain C: H.33, D.34, I.35, F.48, E.49, A.104 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:H.33, C:I.35 Hydrogen bonds: C:D.34, C:D.34, C:E.49 Water bridges: C:N.50 ACT.10: 3 residues within 4Å: Chain C: H.75, T.86, R.87 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.86 Salt bridges: C:H.75 ACT.13: 6 residues within 4Å: Chain D: H.33, D.34, I.35, F.48, E.49, A.104 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:H.33, D:I.35 Hydrogen bonds: D:D.34, D:D.34, D:E.49 Water bridges: D:N.50 ACT.14: 3 residues within 4Å: Chain D: H.75, T.86, R.87 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.86 Salt bridges: D:H.75 ACT.17: 6 residues within 4Å: Chain E: H.33, D.34, I.35, F.48, E.49, A.104 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:H.33, E:I.35 Hydrogen bonds: E:D.34, E:D.34, E:E.49 Water bridges: E:N.50 ACT.18: 3 residues within 4Å: Chain E: H.75, T.86, R.87 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.86 Salt bridges: E:H.75 ACT.21: 6 residues within 4Å: Chain F: H.33, D.34, I.35, F.48, E.49, A.104 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:H.33, F:I.35 Hydrogen bonds: F:D.34, F:D.34, F:E.49 Water bridges: F:N.50 ACT.22: 3 residues within 4Å: Chain F: H.75, T.86, R.87 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.86 Salt bridges: F:H.75

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

NA.3: 11 residues within 4Å: Chain A: F.78, D.80, G.81 Chain B: F.78, D.80, G.81 Chain C: F.78, D.80, G.81 Ligands: NA.7, NA.11 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:G.81, A:G.81, B:G.81 NA.7: 11 residues within 4Å: Chain A: F.78, D.80, G.81 Chain B: F.78, D.80, G.81 Chain C: F.78, D.80, G.81 Ligands: NA.3, NA.11 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:G.81, A:G.81, B:G.81 NA.11: 11 residues within 4Å: Chain A: F.78, D.80, G.81 Chain B: F.78, D.80, G.81 Chain C: F.78, D.80, G.81 Ligands: NA.3, NA.7 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:G.81, A:G.81, B:G.81 NA.15: 11 residues within 4Å: Chain D: F.78, D.80, G.81 Chain E: F.78, D.80, G.81 Chain F: F.78, D.80, G.81 Ligands: NA.19, NA.23 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: E:G.81, F:G.81, D:G.81 NA.19: 11 residues within 4Å: Chain D: F.78, D.80, G.81 Chain E: F.78, D.80, G.81 Chain F: F.78, D.80, G.81 Ligands: NA.15, NA.23 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: E:G.81, F:G.81, D:G.81 NA.23: 11 residues within 4Å: Chain D: F.78, D.80, G.81 Chain E: F.78, D.80, G.81 Chain F: F.78, D.80, G.81 Ligands: NA.15, NA.19 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: E:G.81, F:G.81, D:G.81

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

SO4.4: 5 residues within 4Å: Chain A: R.13 Chain B: R.13 Chain C: R.13 Ligands: SO4.8, SO4.12 15 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C, 6 interactions with chain A Water bridges: B:R.13, B:R.13, B:R.13, B:R.13, B:R.13, C:R.13, C:R.13, A:R.13, A:R.13, A:R.13, A:R.13, A:R.13 Salt bridges: B:R.13, C:R.13, A:R.13 SO4.8: 5 residues within 4Å: Chain A: R.13 Chain B: R.13 Chain C: R.13 Ligands: SO4.4, SO4.12 15 PLIP interactions: 6 interactions with chain B, 6 interactions with chain C, 3 interactions with chain A Water bridges: B:R.13, B:R.13, B:R.13, B:R.13, B:R.13, C:R.13, C:R.13, C:R.13, C:R.13, C:R.13, A:R.13, A:R.13 Salt bridges: B:R.13, C:R.13, A:R.13 SO4.12: 5 residues within 4Å: Chain A: R.13 Chain B: R.13 Chain C: R.13 Ligands: SO4.4, SO4.8 15 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C, 6 interactions with chain A Water bridges: B:R.13, B:R.13, C:R.13, C:R.13, C:R.13, C:R.13, C:R.13, A:R.13, A:R.13, A:R.13, A:R.13, A:R.13 Salt bridges: B:R.13, C:R.13, A:R.13 SO4.16: 5 residues within 4Å: Chain D: R.13 Chain E: R.13 Chain F: R.13 Ligands: SO4.20, SO4.24 15 PLIP interactions: 6 interactions with chain D, 3 interactions with chain F, 6 interactions with chain E Water bridges: D:R.13, D:R.13, D:R.13, D:R.13, D:R.13, F:R.13, F:R.13, E:R.13, E:R.13, E:R.13, E:R.13, E:R.13 Salt bridges: D:R.13, F:R.13, E:R.13 SO4.20: 5 residues within 4Å: Chain D: R.13 Chain E: R.13 Chain F: R.13 Ligands: SO4.16, SO4.24 15 PLIP interactions: 3 interactions with chain D, 6 interactions with chain F, 6 interactions with chain E Water bridges: D:R.13, D:R.13, F:R.13, F:R.13, F:R.13, F:R.13, F:R.13, E:R.13, E:R.13, E:R.13, E:R.13, E:R.13 Salt bridges: D:R.13, F:R.13, E:R.13 SO4.24: 5 residues within 4Å: Chain D: R.13 Chain E: R.13 Chain F: R.13 Ligands: SO4.16, SO4.20 15 PLIP interactions: 6 interactions with chain D, 6 interactions with chain F, 3 interactions with chain E Water bridges: D:R.13, D:R.13, D:R.13, D:R.13, D:R.13, F:R.13, F:R.13, F:R.13, F:R.13, F:R.13, E:R.13, E:R.13 Salt bridges: D:R.13, F:R.13, E:R.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clifton, M.C. et al., The structure of CyaY from Burkholderia cenocepacia. To be Published

Release Date

2013-03-27

Peptides

Protein CyaY: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Protein CyaY