OCA Atlas for 1RZG

1RZG

Immune System

date

Dec 24, 2003

title

Crystal Structure Of Human Anti-Hiv-1 Gp120 Reactive Antibod

authors

C.C.Huang, M.Venturi, S.Majeed, M.J.Moore, S.Phogat, M.Y.Zhang, D.S.Dimitrov, W.A.Hendrickson, J.Robinson, J.Sodroski, R.Wyatt, M.Farzan, P.D.Kwong

compound

source

Molecule: Fab 412d Light Chain
Chain: A, C
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_cell: Immortalized B-Cell Clone Fused Wit Murine B-Cell Fusion Partner;

Molecule: Fab 412d Heavy Chain
Chain: B, D
Engineered: Yes

symmetry

Space Group: P 1 21 1

R_factor

0.201

R_Free

0.251

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
63.088	89.313	85.863	90.00	110.31	90.00

method

X-Ray Diffraction

resolution

2.00 Å

ligand

ASP, CYS, FRU, GLC, TYS

enzyme

related structures

by homologous chain: 1IQD, 1RZ7, 1TJG

Primary reference

Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120., Huang CC, Venturi M, Majeed S, Moore MJ, Phogat S, Zhang MY, Dimitrov DS, Hendrickson WA, Robinson J, Sodroski J, Wyatt R, Choe H, Farzan M, Kwong PD, Proc Natl Acad Sci U S A 2004 Mar 2;101(9):2706-11. Epub 2004 Feb 23. PMID:14981267

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]

Biological Unit Coordinates (1rzg.pdb1.gz) 77 Kb

Biological Unit Coordinates (1rzg.pdb2.gz) 74 Kb

LPC: Ligand-Protein Contacts for 1RZG

CSU: Contacts of Structural Units for 1RZG

Likely Quarternary Molecular Structure file(s) for 1RZG

Structure Factors (993 Kb)

Retrieve 1RZG in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1RZG from S2C, [Save to disk]

Re-refined 1rzg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RZG 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 1RZG

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1RZG, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1rzga1, region A:1-113 [Jmol] [rasmolscript] [script source]
- Domain d1rzga2, region A:114-214 [Jmol] [rasmolscript] [script source]
- Domain d1rzgb1, region B:1-107 [Jmol] [rasmolscript] [script source]
- Domain d1rzgb2, region B:108-213 [Jmol] [rasmolscript] [script source]
- Domain d1rzgc2, region C:114-213 [Jmol] [rasmolscript] [script source]
- Domain d1rzgc1, region C:2-113 [Jmol] [rasmolscript] [script source]
- Domain d1rzgd1, region D:1-107 [Jmol] [rasmolscript] [script source]
- Domain d1rzgd2, region D:108-214 [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1rzg_D] [1rzg_C] [1rzg_B] [1rzg_A] [1rzg]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 1RZG: [IG_like] [IGv ] by SMART

Other resources with information on 1RZG

Community annotation for 1RZG 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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