OCA Atlas for 3MLR

3MLR

Immune System

date

Apr 18, 2010

title

Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex With Peptide

authors

X.P.Kong

compound

source

Molecule: Human Monoclonal Anti-Hiv-1 Gp120 V3 Antibody 255 Light Chain;
Chain: L

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Human Monoclonal Anti-Hiv-1 Gp120 V3 Antibody 255 Heavy Chain;
Chain: H

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Hiv-1 Gp120 Third Variable Region (V3) Crown
Chain: P

Organism_scientific: Human Immunodeficiency Virus Type 1
Organism_common: Hiv-1
Organism_taxid: 11698
Strain: New York-5 Isolate

symmetry

Space Group: P 1

R_factor

0.181

R_Free

0.216

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
42.414	43.076	58.212	87.86	85.50	85.82

method

X-Ray Diffraction

resolution

1.80 Å

Primary reference

Conserved structural elements in the V3 crown of HIV-1 gp120., Jiang X, Burke V, Totrov M, Williams C, Cardozo T, Gorny MK, Zolla-Pazner S, Kong XP, Nat Struct Mol Biol. 2010 Aug;17(8):955-61. Epub 2010 Jul 11. PMID:20622876

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]

Biological Unit Coordinates (3mlr.pdb1.gz) 80 Kb

CSU: Contacts of Structural Units for 3MLR

Structure Factors (463 Kb)

Retrieve 3MLR in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3MLR from S2C, [Save to disk]

Re-refined 3mlr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3MLR 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 3MLR

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 3MLR, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3mlr] [3mlr_L] [3mlr_P] [3mlr_H]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 3MLR: [IG_like] [IGv ] by SMART

Other resources with information on 3MLR

Community annotation for 3MLR 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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