SMTL ID : 5mdo.1 (1 other biounit)

Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: Q.148, Q.151, D.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.151, A:Q.151 NA.2: 4 residues within 4Å: Chain A: D.45, N.46, G.48 Chain C: G.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.48 NA.3: 3 residues within 4Å: Chain A: D.83, P.84, G.87 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:N.153 Hydrogen bonds: A:D.83 NA.11: 4 residues within 4Å: Chain A: G.183 Chain B: D.45, N.46, G.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.45 NA.12: 3 residues within 4Å: Chain B: D.83, P.84, G.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.83, B:G.87 NA.13: 3 residues within 4Å: Chain B: Q.148, Q.151, D.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.151, B:D.176 NA.16: 4 residues within 4Å: Chain B: G.183 Chain C: D.45, N.46, G.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.183 NA.17: 3 residues within 4Å: Chain C: Q.148, Q.151, D.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.148, C:Q.151 NA.18: 3 residues within 4Å: Chain C: D.83, P.84, G.87 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:N.153 Hydrogen bonds: C:P.84

10 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.4: 4 residues within 4Å: Chain A: D.202, G.226, A.239, Q.240 No protein-ligand interaction detected (PLIP) C8E.5: 3 residues within 4Å: Chain A: Y.205, N.221, Y.223 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.209 C8E.6: 5 residues within 4Å: Chain A: N.153, G.173, A.174, Y.186 Chain B: M.50 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.186 C8E.7: 9 residues within 4Å: Chain A: F.280, N.291, S.293, D.294, D.295, D.319, F.320, E.322 Ligands: C8E.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.293 Water bridges: A:D.281 C8E.8: 6 residues within 4Å: Chain A: L.263, L.274, Y.276, D.295, V.297 Ligands: C8E.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.276 Water bridges: A:V.297 C8E.9: 4 residues within 4Å: Chain A: A.261, Y.276 Ligands: C8E.8, C8E.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.261, A:Y.276 C8E.10: 5 residues within 4Å: Chain A: M.259, Y.276, F.280 Ligands: C8E.7, C8E.9 No protein-ligand interaction detected (PLIP) C8E.14: 4 residues within 4Å: Chain B: F.231, N.233, I.235, F.237 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.231, B:F.231, B:I.235, B:F.237, B:F.237 Hydrogen bonds: B:N.233 C8E.15: 12 residues within 4Å: Chain B: M.259, Y.276, F.280, N.291, T.292, S.293, D.294, D.295, D.319, F.320, N.321, E.322 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.291, B:S.293, B:S.293 Water bridges: B:N.291 C8E.19: 4 residues within 4Å: Chain C: F.231, E.232, N.233, F.237 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.237, C:F.237 Hydrogen bonds: C:E.232, C:N.233 Water bridges: C:N.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aunkham, A. et al., Structural basis for chitin acquisition by marine Vibrio species. Nat Commun (2018)

Release Date

2017-12-20

Peptides

Chitoporin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Chitoporin

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