OCA Atlas for 1RZ8

1RZ8

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 17b 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 17b Heavy Chain
Chain: B, D
Engineered: Yes

symmetry

Space Group: P 21 21 21

R_factor

0.212

R_Free

0.262

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
63.212	117.460	154.813	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.30 Å

related structures

by homologous chain: 1G9M, 1I7Z, 1XF3

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] (149 Kb) [Save to disk]

Biological Unit Coordinates (1rz8.pdb1.gz) 73 Kb

Biological Unit Coordinates (1rz8.pdb2.gz) 74 Kb

CSU: Contacts of Structural Units for 1RZ8

Likely Quarternary Molecular Structure file(s) for 1RZ8

Structure Factors (758 Kb)

Retrieve 1RZ8 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1RZ8 from S2C, [Save to disk]

Re-refined 1rz8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RZ8 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 1RZ8

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 1RZ8, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1rz8a1, region A:1-109 [Jmol] [rasmolscript] [script source]
- Domain d1rz8a2, region A:110-212 [Jmol] [rasmolscript] [script source]
- Domain d1rz8b1, region B:1-113 [Jmol] [rasmolscript] [script source]
- Domain d1rz8b2, region B:114-213 [Jmol] [rasmolscript] [script source]
- Domain d1rz8c1, region C:1-109 [Jmol] [rasmolscript] [script source]
- Domain d1rz8c2, region C:110-212 [Jmol] [rasmolscript] [script source]
- Domain d1rz8d1, region D:1-113 [Jmol] [rasmolscript] [script source]
- Domain d1rz8d2, region D:114-213 [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: [1rz8_A] [1rz8_C] [1rz8_D] [1rz8] [1rz8_B]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 1RZ8: [IG_like] [IGv ] by SMART

Other resources with information on 1RZ8

Community annotation for 1RZ8 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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