OCA Atlas for 2QAD

2QAD

Viral Protein Immune System

date

Jun 14, 2007

title

Structure Of Tyrosine-Sulfated 412d Antibody Complexed With Gp120 And Cd4

authors

C.C.Huang, M.Tang, J.Robinson, R.Wyatt, P.D.Kwong

compound

source

Molecule: Envelope Glycoprotein Gp160
Chain: A, E
Fragment: Core With V3
Synonym: Env Polyprotein
Engineered: Yes

Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Strain: Yu2
Gene: Env
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Embryonic Cell Line 293
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Cmvr

Molecule: T-Cell Surface Glycoprotein Cd4
Chain: B, F
Fragment: D1d2, Ig-Like V-Type And Ig-Like C2-Type 1 Domain
Synonym: T-Cell Surface Antigen T4leu-3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Anti-Hiv-1 Antibody 412d Light Chain
Chain: C, G
Fragment: Fab, Antigen-Binding Fragment
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Human Herpesvirus 4
Expression_system_common: Epstein-Barr Virus
Expression_system_taxid: 10376
Expression_system_strain: Epstein-Barr Virus

Molecule: Anti-Hiv-1 Antibody 412d Heavy Chain
Chain: D, H
Fragment: Fab, Antigen-Binding Fragment
Engineered: Yes

symmetry

Space Group: P 1 21 1

R_factor

0.202

R_Free

0.269

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
109.600	53.021	225.326	90.00	104.64	90.00

method

X-Ray Diffraction

resolution

3.30 Å

ligand

EDO, MLA, NAG, TYS

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, E
F, B

Primary reference

Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4., Huang CC, Lam SN, Acharya P, Tang M, Xiang SH, Hussan SS, Stanfield RL, Robinson J, Sodroski J, Wilson IA, Wyatt R, Bewley CA, Kwong PD, Science. 2007 Sep 28;317(5846):1930-4. PMID:17901336

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (651 Kb) [Save to disk]

Biological Unit Coordinates (2qad.pdb1.gz) 325 Kb

Biological Unit Coordinates (2qad.pdb2.gz) 322 Kb

Biological Unit Coordinates (2qad.pdb3.gz) 641 Kb

LPC: Ligand-Protein Contacts for 2QAD

CSU: Contacts of Structural Units for 2QAD

Likely Quarternary Molecular Structure file(s) for 2QAD

Structure Factors (227 Kb)

Retrieve 2QAD in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2QAD from S2C, [Save to disk]

Re-refined 2qad structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2QAD in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 2QAD

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 2QAD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2qad_C] [2qad_H] [2qad_E] [2qad_D] [2qad] [2qad_A] [2qad_B] [2qad_G] [2qad_F]

SWISS-PROT database: [P01730] [P35961] [P01857]

Domain organization of [CD4_HUMAN] [ENV_HV1Y2] [IGHG1_HUMAN] by SWISSPFAM

Domains found in 2QAD: [IG_like] [IGv ] by SMART

Other resources with information on 2QAD

Community annotation for 2QAD at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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