SMTL ID : 2qad.3 (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-2-2-2-2-mer

Ligands

31 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: 6 residues within 4Å: Chain A: N.134, R.274, S.276 Ligands: NAG.28, NAG.30, NAG.35 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.140 Ligand excluded by PLIP NAG.8: 6 residues within 4Å: Chain A: T.136, H.168, N.170, N.243 Ligands: NAG.14, NAG.28 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: 6 residues within 4Å: Chain A: N.170, S.172, R.242, N.243 Ligands: NAG.8, NAG.28 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 NAG.23: 1 residues within 4Å: Chain E: N.73 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain E: D.69, K.70, N.80 Ligand excluded by PLIP NAG.25: 8 residues within 4Å: Chain E: P.51, V.93, N.101, N.215, C.275, S.276, S.277 Ligands: NAG.36 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain E: E.114, N.115 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain E: E.107, E.108, N.128, E.129, Q.182 Ligand excluded by PLIP NAG.28: 8 residues within 4Å: Chain A: R.274 Chain E: N.134, R.274, S.276 Ligands: NAG.6, NAG.8, NAG.14, NAG.35 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain E: N.140 Ligand excluded by PLIP NAG.30: 8 residues within 4Å: Chain E: N.134, T.136, H.168, N.170, N.243, T.245 Ligands: NAG.6, NAG.35 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.194 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain E: N.200, P.201, S.202, R.299 Ligands: NAG.34 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: N.224, T.226 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain E: N.232 Ligands: NAG.32 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain E: N.243 Ligands: NAG.6, NAG.28, NAG.30 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain E: N.101, S.130, N.278 Ligands: NAG.25 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain E: N.293 Ligand excluded by PLIP

4 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 MLA.40: 3 residues within 4Å: Chain F: N.103, S.104, T.115 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.104, F:S.104, F:S.104 MLA.42: 4 residues within 4Å: Chain H: R.38, R.63, E.89, D.90 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:E.89, H:E.89 Salt bridges: H:R.38, H:R.38, H:R.63, H:R.63

7 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) EDO.38: 3 residues within 4Å: Chain E: K.320, I.321, E.322 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.322, E:E.322 EDO.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.41: 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: AE
T-cell surface glycoprotein CD4: BF
anti-HIV-1 antibody 412d light chain: CG
anti-HIV-1 antibody 412d heavy chain: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
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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