SMTL ID : 4ydl.1 (1 other biounit)

Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex with HIV-1 clade AE strain 93TH057gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, L.161, H.220 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 Water bridges: A:N.118 NAG.2: 3 residues within 4Å: Chain A: H.42, N.113, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG.3: 10 residues within 4Å: Chain A: P.96, K.136, V.138, L.145, N.146, N.244, C.306, V.307, S.308 Ligands: NAG.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:N.146, A:S.308 Water bridges: A:R.246 NAG.4: 8 residues within 4Å: Chain A: E.159, N.160 Chain C: Q.27, G.28, I.29, L.30, Q.33 Ligands: NAG.1 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Q.27, C:Q.33, A:N.160 Water bridges: A:N.160, A:T.162 NAG.5: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.153, A:I.154 Water bridges: A:Q.212, A:Q.212 NAG.6: 5 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, V.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.181, A:Y.198 Water bridges: A:N.179, A:N.179 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: T.239, M.240, 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: 8 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.262, M.268, K.269, C.271 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.255 Hydrogen bonds: A:N.259, A:K.269 NAG.10: 4 residues within 4Å: Chain A: N.146, S.175, N.309 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.175, A:N.309 Water bridges: A:S.175, A:S.175 NAG.12: 5 residues within 4Å: Chain C: S.14, E.17, N.104, R.105, T.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.14

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 7 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64, Y.101 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.64, A:D.64

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

SO4.13: 4 residues within 4Å: Chain C: P.60, E.61, R.62, R.78 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.61, C:R.62, C:R.78 Water bridges: C:R.62 Salt bridges: C:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell (2015)

Release Date

2015-06-03

Peptides

Envelope glycoprotein gp160,Envelope glycoprotein gp160: A
HEAVY CHAIN OF ANTIBODY C38-VRC18.02: B
LIGHT CHAIN OF ANTIBODY C38-VRC18.02: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

Envelope glycoprotein gp160,Envelope glycoprotein gp160

HEAVY CHAIN OF ANTIBODY C38-VRC18.02

LIGHT CHAIN OF ANTIBODY C38-VRC18.02

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