SMTL ID : 5w1x.1 (2 other biounits)

Crystal Structure of Humanpapillomavirus18 (HPV18) Capsid L1 Pentamers Bound to Heparin Oligosaccharides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.37 Å

Oligo State

homo-pentamer

Ligands

9 x JHM- IDS: 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose(Non-covalent)(Non-functional Binders)

JHM-IDS.1: 7 residues within 4Å: Chain A: R.159, S.162, D.165 Chain E: G.37, G.38, N.39, K.343 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Salt bridges: E:K.343, A:R.159 Hydrogen bonds: A:S.162, A:S.162, A:D.165 JHM-IDS.4: 2 residues within 4Å: Chain A: N.402, K.406 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.406, A:N.402 Salt bridges: A:K.406, A:K.406 JHM-IDS.5: 3 residues within 4Å: Chain A: G.335 Chain C: Q.254 Ligands: JHM-IDS-JHM-IDS.7 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.254, A:G.335 JHM-IDS.6: 6 residues within 4Å: Chain A: Q.254, K.259, G.260 Chain D: G.335, Q.336 Ligands: JHM-IDS.11 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Salt bridges: A:K.259, A:K.259 Hydrogen bonds: D:G.335 JHM-IDS.8: 2 residues within 4Å: Chain C: T.76, T.364 No protein-ligand interaction detected (PLIP) JHM-IDS.10: 4 residues within 4Å: Chain D: P.34 Chain E: T.251, Q.254 Ligands: JHM-IDS-JHM-IDS.9 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.254 JHM-IDS.11: 1 residues within 4Å: Ligands: JHM-IDS.6 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.341 JHM-IDS.12: 5 residues within 4Å: Chain D: K.259, T.261, G.262, A.265 Ligands: JHM-IDS-JHM-IDS.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.260, D:G.262 Salt bridges: D:K.259 JHM-IDS.15: 5 residues within 4Å: Chain E: P.394, Y.395, K.397, L.398 Ligands: JHM-IDS-JHM-IDS.14 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.397, E:L.398

6 x JHM- IDS- JHM- IDS: 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose

JHM-IDS-JHM-IDS.2: 4 residues within 4Å: Chain A: Q.330, S.331, P.332, K.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.331, A:Q.330 JHM-IDS-JHM-IDS.3: 2 residues within 4Å: Chain A: K.40, Q.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.41 JHM-IDS-JHM-IDS.7: 15 residues within 4Å: Chain A: V.333 Chain B: Y.30, F.31, R.32, K.45, S.192, D.196, K.198, Q.207, S.208, I.209 Chain C: P.253, S.255, I.258 Ligands: JHM-IDS.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.32, C:S.255 Salt bridges: B:K.45 JHM-IDS-JHM-IDS.9: 4 residues within 4Å: Chain C: G.335 Chain E: Q.254, K.259 Ligands: JHM-IDS.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.335 JHM-IDS-JHM-IDS.13: 5 residues within 4Å: Chain B: G.335, Q.336 Chain D: Q.254, K.259 Ligands: JHM-IDS.12 No protein-ligand interaction detected (PLIP) JHM-IDS-JHM-IDS.14: 6 residues within 4Å: Chain E: G.153, T.154, A.155, K.157, K.172 Ligands: JHM-IDS.15 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.157 Hydrogen bonds: E:A.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dasgupta, J. et al., Structural basis of oligosaccharide receptor recognition by human papillomavirus. J. Biol. Chem. (2011)

Release Date

2018-12-12

Peptides

Major capsid protein L1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Major capsid protein L1

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