SMTL ID : 4h8w.1

Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with HIV-1 clade A/E gp120 and sCD4.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 2 residues within 4Å: Chain A: E.44, N.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.44, A:N.45 Water bridges: A:E.44, A:E.44 NAG.2: 4 residues within 4Å: Chain A: N.118, T.120, I.156, H.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.118 NAG.3: 3 residues within 4Å: Chain A: N.113, K.115, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.115, A:K.115 NAG.4: 10 residues within 4Å: Chain A: D.95, P.96, K.136, L.145, N.146, N.244, R.246, C.306, V.307, S.308 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:S.308 Water bridges: A:K.136, A:K.136, A:V.307 NAG.5: 4 residues within 4Å: Chain A: N.160, T.162, N.163 Chain D: K.90 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:N.160, D:K.90 Water bridges: A:T.162, A:N.163, A:N.163, A:N.164, D:K.29, D:K.29 NAG.6: 5 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.216 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.154, A:N.173, A:K.216, A:K.216 Water bridges: A:N.173, A:Q.212 NAG.7: 4 residues within 4Å: Chain A: N.179, T.181, E.200, K.303 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.200, A:K.303 Water bridges: A:N.179, A:N.179, A:N.179, A:N.179, A:T.181 NAG.8: 2 residues within 4Å: Chain A: N.202, K.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.202, A:K.205 NAG.9: 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 Water bridges: A:T.255, A:T.255 NAG.10: 5 residues within 4Å: Chain A: T.255, Q.256, N.259, C.262, C.271 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.255 Hydrogen bonds: A:N.259, A:C.271, A:C.271

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.11: 7 residues within 4Å: Chain A: V.1, W.2, L.43, V.108, L.110, S.128, I.352 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.2, A:L.43, A:V.108, A:L.110, A:I.352, A:I.352 Hydrogen bonds: A:S.128 MRD.12: 10 residues within 4Å: Chain A: V.139, T.141, E.237, S.242, F.243, F.249, I.285, N.286, M.287, W.288 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.141, A:I.285, A:W.288 Hydrogen bonds: A:S.242 Water bridges: A:F.243, A:W.288 MRD.13: 8 residues within 4Å: Chain B: G.42, K.43, G.44 Chain C: A.8, D.87, Y.89, G.104, G.105 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.8 Hydrogen bonds: C:D.87

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Acharya, P. et al., Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection. J.Virol. (2014)

Release Date

2014-04-09

Peptides

HIV-1 CLADE A/E 93TH057 (H375S) GP120: A
FAB HEAVY CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5: B
FAB LIGHT CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5: C
T-cell surface glycoprotein CD4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

D
C

HIV-1 CLADE A/E 93TH057 (H375S) GP120

FAB HEAVY CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5

FAB LIGHT CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5

T-cell surface glycoprotein CD4

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