SMTL ID : 6vlw.1

Crystal Structure of 426cOD in Complex with VRC01 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.42 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-BMA.1: 4 residues within 4Å: Chain B: I.20, S.63, W.65, N.70 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: G.9, Q.10, M.11, P.116, I.118, P.155 No protein-ligand interaction detected (PLIP)

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: T.91, I.118 Ligand excluded by PLIP CL.4: 7 residues within 4Å: Chain A: V.177, S.185, L.186, S.187 Chain B: S.158, S.172, T.174 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: S.128, V.129, V.215 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: H.172 Chain B: T.160, D.163 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: K.43, R.44 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: P.10, R.12, N.166 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: N.22, G.73, L.75 Ligands: NAG.14 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain C: G.146, G.147 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 5 residues within 4Å: Chain A: Q.179, S.180 Chain B: N.154, Q.156, T.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.180 SO4.10: 1 residues within 4Å: Chain C: R.12 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.12

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

NA.9: 4 residues within 4Å: Chain B: Q.151, L.177, D.181, H.185 No protein-ligand interaction detected (PLIP)

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

NAG.14: 5 residues within 4Å: Chain C: N.22, S.101, E.103 Ligands: CL.12, NAG.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.22 NAG.15: 6 residues within 4Å: Chain C: P.10, L.149, T.152, T.153, N.166, S.168 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.152 Hydrogen bonds: C:N.166 NAG.16: 6 residues within 4Å: Chain C: K.20, S.21, N.22, N.72, N.157 Ligands: NAG.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, Y.R. et al., HIV-1 VRC01 Germline-Targeting Immunogens Select Distinct Epitope-Specific B Cell Receptors. Immunity (2020)

Release Date

2020-12-09

Peptides

VRC01 Fab Heavy Chain: A
VRC01 Fab Light Chain: B
426cOD: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
G

VRC01 Fab Heavy Chain

VRC01 Fab Light Chain

426cOD

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