1Q1J	Immune System	date	Jul 21, 2003
title	Crystal Structure Analysis Of Anti-Hiv-1 Fab 447-52d In Comp V3 Peptide
authors	R.L.Stanfield, M.K.Gorny, C.Williams, S.Zolla-Pazner, I.A.Wilson
compound		source
Molecule: Fab 447-52d, Light Chain Chain: L, M		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Other_details: Isolated From Peripheral Blood Cells
Molecule: Fab 447-52d, Heavy Chain Chain: H, I		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Other_details: Isolated From Peripheral Blood Cells
Molecule: Gp120 V3 Peptide Chain: P, Q Engineered: Yes		Synthetic: Yes Other_details: This Sequence Occurs In Hiv-1 Gp120
symmetry	Space Group: P 1 21 1	R_factor 0.250 R_Free 0.285
crystal cell	length a length b length c angle alpha angle beta angle gamma 76.673 74.903 100.047 90.00 100.57 90.00
method	X-Ray Diffraction	resolution	2.50 Å
related structures	by homologous chain: 1CLY, 1LIL, 4BJL
Primary reference	Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D., Stanfield RL, Gorny MK, Williams C, Zolla-Pazner S, Wilson IA, Structure (Camb) 2004 Feb;12(2):193-204. PMID:14962380

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk] Biological Unit Coordinates (1q1j.pdb1.gz) 137 Kb CSU: Contacts of Structural Units for 1Q1J Likely Quarternary Molecular Structure file(s) for 1Q1J Structure Factors (610 Kb) Retrieve 1Q1J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1Q1J from S2C, [Save to disk] Re-refined 1q1j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1Q1J 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 1Q1J

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 1Q1J, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1q1jh1, region H:1-113 [Jmol] [rasmolscript] [script source]     - Domain d1q1jh2, region H:114-227 [Jmol] [rasmolscript] [script source]     - Domain d1q1ji1, region I:1-113 [Jmol] [rasmolscript] [script source]     - Domain d1q1ji2, region I:114-227 [Jmol] [rasmolscript] [script source]     - Domain d1q1jl1, region L:1-108 [Jmol] [rasmolscript] [script source]     - Domain d1q1jl2, region L:109-213 [Jmol] [rasmolscript] [script source]     - Domain d1q1jm1, region M:1-108 [Jmol] [rasmolscript] [script source]     - Domain d1q1jm2, region M:109-213 [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: [1q1j] [1q1j_I] [1q1j_H] [1q1j_P] [1q1j_M] [1q1j_L] [1q1j_Q] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 1Q1J: [IG_like] [IGv ] by SMART

Other resources with information on 1Q1J

Community annotation for 1Q1J at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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