SMTL ID : 4lsr.1

Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E stran 93TH057 gp120 with LOOP D and Loop V5 from clade A strain KER_2018_11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, P.122, S.158, H.220 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.118, A:T.120, A:T.120 NAG.2: 11 residues within 4Å: Chain A: D.95, P.96, K.136, L.145, N.146, F.243, N.244, R.246, C.306, V.307, S.308 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.145, A:F.243 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 NAG.3: 9 residues within 4Å: Chain A: E.159, N.160, S.162 Chain C: G.28, I.29, G.30, D.32, Q.90, Y.91 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.91 Hydrogen bonds: C:G.28, C:D.32, C:D.32, A:N.160, A:S.162 Water bridges: C:G.30, C:K.31 NAG.4: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 Ligands: SO4.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.153, A:I.154, A:N.173, A:K.216, A:K.216 NAG.5: 7 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, K.303, N.305, V.307 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:N.179, A:Y.198, A:Y.198, A:K.303 Water bridges: A:T.181, A:E.200 NAG.6: 4 residues within 4Å: Chain A: N.202, T.204, K.205 Ligands: SO4.13 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: E.215, N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.215 NAG.8: 3 residues within 4Å: Chain A: T.239, N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 Water bridges: A:T.255 NAG.9: 4 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.255 Hydrogen bonds: A:N.259

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

SO4.10: 3 residues within 4Å: Chain A: K.208, Q.212 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.212 Salt bridges: A:K.208 SO4.11: 4 residues within 4Å: Chain A: A.15, K.16, A.17, H.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.17, A:H.18 Salt bridges: A:H.18 SO4.12: 4 residues within 4Å: Chain A: W.26, A.30, S.67, Q.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.67, A:S.67, A:Q.71 SO4.13: 3 residues within 4Å: Chain A: K.174, K.205 Ligands: NAG.6 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.174, A:K.205, A:K.208 SO4.14: 3 residues within 4Å: Chain B: A.10, V.11, R.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.11 Water bridges: B:R.12 Salt bridges: B:R.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies. Immunity (2013)

Release Date

2013-08-21

Peptides

ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN ker_2018_11: A
HEAVY CHAIN OF ANTIBODY VRC-CH31: B
LIGHT CHAIN OF ANTIBODY VRC-CH31 (N70D MUTATION): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN ker_2018_11

HEAVY CHAIN OF ANTIBODY VRC-CH31

LIGHT CHAIN OF ANTIBODY VRC-CH31 (N70D MUTATION)

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