SMTL ID : 6mft.1 (1 other biounit)

Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01 A60C heavy chain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG.1: 10 residues within 4Å: Chain B: Q.27, S.28, V.29, S.30, Y.32, G.68, Y.91 Chain C: K.120, N.160, S.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.27, B:S.28, B:S.30 NAG-NAG.2: 5 residues within 4Å: Chain C: L.236, T.239, T.240, N.253, S.255 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.3: 14 residues within 4Å: Chain C: E.19, E.21, T.93, D.95, P.96, K.136, V.138, L.145, N.146, F.243, N.244, C.298, K.299, S.300 No protein-ligand interaction detected (PLIP)

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 4 residues within 4Å: Chain C: E.40, V.42, N.113, N.125 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.40 NAG.5: 8 residues within 4Å: Chain C: E.152, E.153, I.154, N.173, K.174, Q.212, K.215, K.216 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.154, C:N.173, C:Q.212 NAG.6: 6 residues within 4Å: Chain C: G.256, N.259, T.261, I.262, S.263, I.267 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.267 Hydrogen bonds: C:N.259, C:T.261, C:S.263 Water bridges: C:T.261 NAG.7: 5 residues within 4Å: Chain A: Q.65 Chain C: Q.229, N.316, T.318, I.320 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.229, C:Q.229, C:T.318 Water bridges: C:D.260, C:D.260 NAG.8: 3 residues within 4Å: Chain C: N.114, T.116, N.124 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.114, C:N.124 NAG.9: 3 residues within 4Å: Chain C: K.174, S.202, N.205 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.174, C:N.205 NAG.10: 3 residues within 4Å: Chain A: S.75 Chain C: N.81, T.82 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.77

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 13 residues within 4Å: Chain A: S.55 Chain C: V.139, S.140, T.141, E.237, I.238, S.242, F.243, N.278, M.279, W.280, G.326, M.328 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Water bridges: C:V.139, C:M.279, C:M.279, C:W.280, A:N.54, A:N.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borst, A.J. et al., Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. Elife (2018)

Release Date

2018-11-14

Peptides

Heavy Chain glVRC01: A
Light chain glVRC01: B
Gp120: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
G

Heavy Chain glVRC01

Light chain glVRC01

Gp120

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