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

Crystal structure of broadly and potently neutralizing antibody 44-VRC13.01 in complex with HIV-1 clade AE strain 93TH057 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 8 residues within 4Å: Chain A: F.117, N.118, T.120, G.121, P.122, S.158, L.161, H.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.120, A:T.120 NAG.2: 4 residues within 4Å: Chain A: H.42, N.113, K.115, N.125 No protein-ligand interaction detected (PLIP) NAG.3: 12 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, L.145, N.146, F.243, N.244, C.306, V.307, S.308 Ligands: NAG.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:K.136, A:S.308 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.160 NAG.5: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.154, A:Q.212, A:Q.212 NAG.6: 6 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, N.305, V.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.200, A:N.305 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.205 NAG.8: 7 residues within 4Å: Chain A: M.240, N.253, T.255 Chain B: F.34, T.36, S.59, T.60 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.59, A:N.253 NAG.9: 6 residues within 4Å: Chain A: K.136, N.146, L.149, S.175, N.309 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:N.309 NAG.10: 2 residues within 4Å: Chain B: N.90, T.92 No protein-ligand interaction detected (PLIP) NAG.13: 5 residues within 4Å: Chain C: S.17, I.18, N.19, S.61, T.70 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.19, C:N.19

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.11: 3 residues within 4Å: Chain B: S.149, S.150, K.151 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.150 IPA.14: 8 residues within 4Å: Chain C: E.79, V.99, R.101, Y.134, G.136, K.160, N.164, Y.166 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.134, C:Y.166 Hydrogen bonds: C:Y.134 Water bridges: C:N.164

1 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.12: 8 residues within 4Å: Chain B: L.211, G.212, T.213, Q.214, T.215, K.232, E.234, P.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.215, B:K.232

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

NA.15: 9 residues within 4Å: Chain B: L.146, L.163 Chain C: F.112, P.113, P.114, S.115, E.118, T.125, V.127 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.115, C:T.125

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 44-VRC13.01: B
LIGHT CHAIN OF ANTIBODY 44-VRC13.01: 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 44-VRC13.01

LIGHT CHAIN OF ANTIBODY 44-VRC13.01

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