SMTL ID : 7eqr.1 (1 other biounit)

Crystal structure of Truncated (Delta 1-19) Chitoporin VhChiP from Vibrio harveyi in complex with chitohexaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-trimer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 13 residues within 4Å: Chain A: E.34, R.36, Y.60, R.75, D.103, W.104, N.108, Q.279, M.281, Y.291, R.293, E.328, Y.330 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.60, A:R.75, A:D.103, A:D.103, A:R.293 Water bridges: A:R.75, A:N.108, A:N.108, A:R.129

1 x NAG- NAG- NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-NAG-NAG-NAG.2: 17 residues within 4Å: Chain B: N.32, E.34, R.36, Y.60, F.65, R.75, Y.99, D.103, W.104, N.108, W.117, D.128, Y.291, W.312, N.317, E.328, Y.330 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.65 Hydrogen bonds: B:W.312, B:N.317, B:N.317

1 x NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-NAG.3: 13 residues within 4Å: Chain C: N.32, E.34, R.36, Y.60, F.65, R.75, Y.99, D.103, D.116, W.117, D.128, W.312, N.317 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.65 Hydrogen bonds: C:N.317

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.4: 3 residues within 4Å: Chain A: F.65, W.312, N.317 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.65 Hydrogen bonds: A:N.317, A:N.317

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

C8E.5: 6 residues within 4Å: Chain A: V.204, Q.219, Y.220, D.236, M.238, F.259 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.220, A:F.259, A:F.259, A:F.259 C8E.6: 2 residues within 4Å: Chain A: L.175, L.178 No protein-ligand interaction detected (PLIP) C8E.7: 5 residues within 4Å: Chain A: N.270, S.272, D.273, D.274, D.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.272 C8E.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) C8E.13: 7 residues within 4Å: Chain B: D.14, Y.15, D.16, N.297, D.298, D.319, N.321 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.16, B:D.319 Hydrogen bonds: B:D.319 C8E.14: 3 residues within 4Å: Chain B: Y.184, N.200, Y.202 No protein-ligand interaction detected (PLIP) C8E.15: 8 residues within 4Å: Chain B: A.218, M.238, A.240, L.242, L.253, G.254, Y.255, V.276 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.240, B:Y.255 C8E.19: 2 residues within 4Å: Chain C: L.178, F.210 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.210, C:F.210 C8E.20: 10 residues within 4Å: Chain C: V.204, G.205, V.206, A.218, Q.219, Y.220, D.236, M.238, F.259 Ligands: C8E.25 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.206, C:M.238 Hydrogen bonds: C:D.236 C8E.21: 6 residues within 4Å: Chain C: I.169, A.182, A.183, Y.184, N.200, Y.202 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.169, C:Y.184, C:Y.184 Hydrogen bonds: C:Y.202 C8E.22: 3 residues within 4Å: Chain C: K.144, Y.173, L.175 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.173, C:L.175 C8E.23: 4 residues within 4Å: Chain A: F.331 Chain C: E.1, V.2, W.54 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.2 C8E.24: 5 residues within 4Å: Chain C: V.151, Y.165, G.167, Y.184, R.188 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.151 Hydrogen bonds: C:Y.184, C:R.188 C8E.25: 3 residues within 4Å: Chain C: M.238, F.259 Ligands: C8E.20 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.259

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

NA.9: 3 residues within 4Å: Chain A: Q.127, Q.130, D.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.130, A:D.155 NA.10: 4 residues within 4Å: Chain A: D.298, F.299, E.301, D.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.298, A:F.299 NA.11: 6 residues within 4Å: Chain A: D.24, N.25, G.27 Chain C: A.157, G.162, D.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.24 NA.12: 4 residues within 4Å: Chain A: D.62, P.63, G.66, G.67 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.132, C:G.158 NA.16: 3 residues within 4Å: Chain B: Q.127, Q.130, D.155 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.127 NA.17: 6 residues within 4Å: Chain A: A.157, G.162, D.163 Chain B: D.24, N.25, G.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.27 NA.18: 4 residues within 4Å: Chain B: D.298, F.299, E.301, D.319 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.299, B:E.301, B:E.301 NA.26: 3 residues within 4Å: Chain C: Q.127, Q.130, D.155 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.155 NA.27: 4 residues within 4Å: Chain C: D.298, F.299, E.301, D.319 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aunkham, A. et al., Structure of truncated VhChiP complex with chitohexaose. To Be Published

Release Date

2022-08-10

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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