SMTL ID : 2qad.1 (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

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

NAG.1: 2 residues within 4Å: Chain A: N.73, T.75 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.80 Ligand excluded by PLIP NAG.3: 9 residues within 4Å: Chain A: P.51, R.91, V.93, L.100, N.101, N.215, C.275, S.276, S.277 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.115, T.117, N.118 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: E.107, E.108, I.109, N.128, Q.182 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.134, R.274, S.276 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.140 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: T.136, H.168, N.170, N.243 Ligands: NAG.14 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, S.203, R.299 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.224, T.226, Q.227 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: I.198, F.199, N.200, N.232, R.235 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.238, N.243 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.170, S.172, R.242, N.243 Ligands: NAG.8 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: R.91, N.101, S.130, N.278 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.293 Ligand excluded by PLIP

2 x MLA: MALONIC ACID(Non-covalent)

MLA.17: 1 residues within 4Å: Chain A: R.143 No protein-ligand interaction detected (PLIP) MLA.19: 4 residues within 4Å: Chain B: K.2, V.3, V.4, K.166 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:K.2, B:K.2, B:K.166, B:K.166

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

EDO.18: 5 residues within 4Å: Chain A: K.188, N.193, N.194, K.195, T.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.188, A:K.188 EDO.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.21: 2 residues within 4Å: Chain C: Q.27, S.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.28 EDO.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

D
D

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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