SMTL ID : 7x5p.1

Truncated VhChiP (1-19aa) in complex with doxycycline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-hexamer

Ligands

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

C8E.1: 6 residues within 4Å: Chain A: I.169, A.182, A.183, Y.184, N.200, Y.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.200 C8E.6: 7 residues within 4Å: Chain B: Q.9, E.34, M.281, Y.291, R.293, E.328, Y.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.34, B:R.293, B:Y.330 C8E.7: 4 residues within 4Å: Chain B: Q.219, Y.220, M.238, F.259 No protein-ligand interaction detected (PLIP) C8E.12: 9 residues within 4Å: Chain C: Q.9, N.108, Q.279, M.281, V.289, Y.291, R.293, E.328, Y.330 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.9, C:R.293, C:R.293 C8E.13: 10 residues within 4Å: Chain C: I.5, R.40, E.57, Y.60, R.75, Y.99, D.103, D.128, Y.330 Ligands: DXT.11 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.330, C:Y.330 Hydrogen bonds: C:R.36, C:R.75, C:R.75, C:D.103, C:D.128 C8E.14: 3 residues within 4Å: Chain C: Y.184, N.200, Y.202 No protein-ligand interaction detected (PLIP) C8E.15: 7 residues within 4Å: Chain B: L.159 Chain C: R.13, Y.15, L.26, F.65, N.317 Ligands: DXT.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.13, C:R.13, C:Y.15, C:N.317 C8E.19: 7 residues within 4Å: Chain D: Q.9, N.108, M.281, Y.291, R.293, E.328, Y.330 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.9, D:N.108, D:R.293, D:R.293 C8E.20: 7 residues within 4Å: Chain D: V.204, V.206, Q.219, Y.220, D.236, M.238, F.259 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.204, D:V.206, D:M.238 C8E.21: 4 residues within 4Å: Chain D: I.169, Y.184, N.200, Y.202 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.169 Hydrogen bonds: D:N.200 C8E.22: 10 residues within 4Å: Chain D: I.5, R.40, Y.60, R.75, Y.99, D.103, D.128, R.129, Y.330 Ligands: DXT.18 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.330, D:Y.330 Hydrogen bonds: D:Y.60, D:R.75, D:R.75, D:Y.99, D:R.129 C8E.27: 5 residues within 4Å: Chain E: Q.9, E.34, M.281, Y.291, R.293 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.34, E:R.293 C8E.28: 4 residues within 4Å: Chain E: P.177, L.178, F.210 Ligands: C8E.29 No protein-ligand interaction detected (PLIP) C8E.29: 5 residues within 4Å: Chain E: F.210, N.212, I.214, F.216 Ligands: C8E.28 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.212 C8E.32: 5 residues within 4Å: Chain F: E.34, M.281, Y.291, R.293, E.328 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.293, F:R.293

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

NA.2: 5 residues within 4Å: Chain A: Q.127, D.128, R.129, Q.130, D.155 Ligand excluded by PLIP NA.3: 2 residues within 4Å: Chain A: D.137, D.148 Ligand excluded by PLIP NA.4: 5 residues within 4Å: Chain A: D.24, N.25, G.27 Chain C: A.157, G.162 Ligand excluded by PLIP NA.8: 4 residues within 4Å: Chain B: Q.127, D.128, Q.130, D.155 Ligand excluded by PLIP NA.9: 2 residues within 4Å: Chain B: D.137, D.148 Ligand excluded by PLIP NA.10: 5 residues within 4Å: Chain A: A.157, G.162 Chain B: D.24, N.25, G.27 Ligand excluded by PLIP NA.16: 4 residues within 4Å: Chain C: Q.127, D.128, Q.130, D.155 Ligand excluded by PLIP NA.17: 2 residues within 4Å: Chain C: D.137, D.148 Ligand excluded by PLIP NA.23: 2 residues within 4Å: Chain D: D.137, D.148 Ligand excluded by PLIP NA.24: 8 residues within 4Å: Chain D: Q.30, D.62, P.63, S.64, F.65, G.66 Chain E: N.132, G.158 Ligand excluded by PLIP NA.25: 3 residues within 4Å: Chain D: Q.127, Q.130, D.155 Ligand excluded by PLIP NA.30: 5 residues within 4Å: Chain E: Q.127, D.128, R.129, Q.130, D.155 Ligand excluded by PLIP NA.31: 2 residues within 4Å: Chain E: D.137, D.148 Ligand excluded by PLIP NA.33: 3 residues within 4Å: Chain F: Q.127, Q.130, D.155 Ligand excluded by PLIP NA.34: 5 residues within 4Å: Chain D: A.157, G.162 Chain F: D.24, N.25, G.27 Ligand excluded by PLIP NA.35: 3 residues within 4Å: Chain F: D.137, S.146, D.148 Ligand excluded by PLIP

4 x DXT: (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE(Non-covalent)

DXT.5: 8 residues within 4Å: Chain B: Y.60, R.93, Y.99, D.103, W.117, D.128, R.129, W.312 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.117, B:W.117, B:W.312 Hydrogen bonds: B:Y.60, B:Y.60, B:Y.99, B:D.128, B:R.129 Salt bridges: B:D.128 pi-Stacking: B:W.117 DXT.11: 5 residues within 4Å: Chain C: W.117, D.128, W.312 Ligands: C8E.13, C8E.15 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.312 Hydrogen bonds: C:D.128, C:D.128 pi-Stacking: C:W.312 DXT.18: 4 residues within 4Å: Chain D: W.117, D.128, W.312 Ligands: C8E.22 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.312, D:W.312 Salt bridges: D:D.128 pi-Stacking: D:W.312 DXT.26: 8 residues within 4Å: Chain E: Y.60, R.93, Y.99, D.103, W.117, D.128, R.129, W.312 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:W.117, E:W.117, E:W.312 Hydrogen bonds: E:Y.60, E:R.75, E:Y.99, E:D.128, E:D.128, E:R.129, E:R.129 Salt bridges: E:D.128 pi-Stacking: E:W.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aunkham, A. et al., Structure and function of truncated VhChiP. To Be Published

Release Date

2023-03-08

Peptides

Chitoporin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

D
A

E
B

F
E

Membrane

We predict this structure to be a membrane protein.
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Chitoporin

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