SMTL ID : 5w1x.2 (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

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

JHM-IDS-JHM-IDS-JHM-IDS.1: 12 residues within 4Å: Chain A: R.159, P.160, L.161, S.162, Q.163, G.164, T.247, S.266 Chain E: G.38, T.329, T.340, K.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.266

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

JHM-IDS-JHM-IDS-JHM-IDS-JHM-IDS-JHM-IDS.2: 6 residues within 4Å: Chain A: G.38, K.40, Q.41, N.402, K.406 Chain B: R.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.406 Salt bridges: A:K.406

2 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.3: 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 JHM-IDS-JHM-IDS.4: 10 residues within 4Å: Chain A: V.333, P.334 Chain B: K.45, K.198, Q.207, S.208 Chain C: Q.254, S.255, Y.257, I.258 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.208, C:S.255 Salt bridges: B:K.45

4 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.5: 8 residues within 4Å: Chain A: S.156, R.159, C.166, P.167, P.168 Chain E: N.39, K.40, Q.41 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:N.39, A:S.156, A:R.159 Salt bridges: E:K.40 JHM-IDS.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) JHM-IDS.7: 1 residues within 4Å: Ligands: JHM-IDS.8 No protein-ligand interaction detected (PLIP) JHM-IDS.8: 2 residues within 4Å: Chain E: K.172 Ligands: JHM-IDS.7 No protein-ligand interaction detected (PLIP)

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
F

B
G

C
H

D
I

E
J

Major capsid protein L1

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