SMTL ID : 2qad.2 (2 other biounits)

Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.73 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: D.69, K.70, N.80 Ligand excluded by PLIP NAG.3: 8 residues within 4Å: Chain A: P.51, V.93, N.101, N.215, C.275, S.276, S.277 Ligands: NAG.14 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: E.114, N.115 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: E.107, E.108, N.128, E.129, Q.182 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.134, R.274, S.276 Ligands: NAG.13 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.140 Ligand excluded by PLIP NAG.8: 7 residues within 4Å: Chain A: N.134, T.136, H.168, N.170, N.243, T.245 Ligands: NAG.13 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.194 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: N.200, P.201, S.202, R.299 Ligands: NAG.12 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.224, T.226 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.232 Ligands: NAG.10 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.243 Ligands: NAG.6, NAG.8 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.101, S.130, N.278 Ligands: NAG.3 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.293 Ligand excluded by PLIP

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

EDO.16: 3 residues within 4Å: Chain A: K.320, I.321, E.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.322, A:E.322 EDO.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x MLA: MALONIC ACID(Non-covalent)

MLA.18: 3 residues within 4Å: Chain B: N.103, S.104, T.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.104, B:S.104, B:S.104 MLA.20: 4 residues within 4Å: Chain D: R.38, R.63, E.89, D.90 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.89, D:E.89 Salt bridges: D:R.38, D:R.38, D:R.63, D:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.-C. et al., Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science (2007)

Release Date

2007-09-25

Peptides

Envelope glycoprotein gp160: A
T-cell surface glycoprotein CD4: B
anti-HIV-1 antibody 412d light chain: C
anti-HIV-1 antibody 412d heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Envelope glycoprotein gp160

T-cell surface glycoprotein CD4

anti-HIV-1 antibody 412d light chain

anti-HIV-1 antibody 412d heavy chain

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