OCA Atlas for 3MLS

3MLS

Immune System

date

Apr 18, 2010

title

Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex W Gp120 V3 Mimotope

authors

X.P.Kong

compound

source

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

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

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

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Rationally Designed V3 Mimotope
Chain: P, Q, R, S
Engineered: Yes

Synthetic: Yes

symmetry

Space Group: C 1 2 1

R_factor

0.216

R_Free

0.274

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
168.746	43.051	274.341	90.00	94.20	90.00

method

X-Ray Diffraction

resolution

2.50 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] (302 Kb) [Save to disk]

Biological Unit Coordinates (3mls.pdb1.gz) 79 Kb

Biological Unit Coordinates (3mls.pdb2.gz) 78 Kb

Biological Unit Coordinates (3mls.pdb3.gz) 79 Kb

Biological Unit Coordinates (3mls.pdb4.gz) 79 Kb

CSU: Contacts of Structural Units for 3MLS

Structure Factors (1447 Kb)

Retrieve 3MLS in mmCIF format [Save to disk]

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

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

View 3MLS 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 3MLS

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 3MLS, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3mls_S] [3mls_L] [3mls_I] [3mls] [3mls_N] [3mls_K] [3mls_O] [3mls_M] [3mls_R] [3mls_P] [3mls_J] [3mls_Q] [3mls_H]

SWISS-PROT database:

Domain organization of by SWISSPFAM

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

Other resources with information on 3MLS

Community annotation for 3MLS 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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