OCA Atlas for 1E6J

1E6J

Viral Protein

date

Aug 18, 2000

title

Crystal Structure Of Hiv-1 Capsid Protein (P24) In Complex W Fab13b5

authors

C.Berthet-Colominas, S.Monaco, A.Novelli, G.Sibai, F.Mallet, S.Cu

compound

source

Molecule: Immunoglobulin
Chain: H
Fragment: Heavy Chain 1-219
Other_details: Obtained By Papain Cleavage (Fab)

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Immunoglobulin
Chain: L
Fragment: Light Chain 1-210
Other_details: Obtained By Papain Cleavage (Fab)

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Capsid Protein P24
Chain: P
Fragment: Gag Polyprotein Residues 143-352
Synonym: Ca
Engineered: Yes
Other_details: His6 Tag At N-Term, Pro1 And Ile2 Deleted, C Modified

Organism_scientific: Hiv-1 M\:B_hxb2r
Organism_taxid: 11706
Variant: Clone 12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: See Reference 2

symmetry

Space Group: C 1 2 1

R_factor

0.210

R_Free

0.284

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
193.080	45.600	132.470	90.00	132.41	90.00

method

X-Ray Diffraction

resolution

3.00 Å

note

1E6J (Molecule of the Month:pdb163)

related structures

by homologous chain: 1A43, 1ACY, 1AE6, 1BMX, 1GWP, 3CK0

Gene
Ontology

Chain	Function	Process	Component
P

Primary reference

Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24., Monaco-Malbet S, Berthet-Colominas C, Novelli A, Battai N, Piga N, Cheynet V, Mallet F, Cusack S, Structure. 2000 Oct 15;8(10):1069-77. PMID:11080628

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk]

Biological Unit Coordinates (1e6j.pdb1.gz) 101 Kb

CSU: Contacts of Structural Units for 1E6J

Likely Quarternary Molecular Structure file(s) for 1E6J

Structure Factors (109 Kb)

Retrieve 1E6J in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1E6J from S2C, [Save to disk]

Re-refined 1e6j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1E6J 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 1E6J

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 1E6J, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1e6jh1, region H:1-120 [Jmol] [rasmolscript] [script source]
- Domain d1e6jh2, region H:121-219 [Jmol] [rasmolscript] [script source]
- Domain d1e6jl1, region L:1-105 [Jmol] [rasmolscript] [script source]
- Domain d1e6jl2, region L:106-210 [Jmol] [rasmolscript] [script source]
- Domain d1e6jp2, region P:11-147 [Jmol] [rasmolscript] [script source]
- Domain d1e6jp1, region P:148-220 [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: [1e6j_L] [1e6j_P] [1e6j_H] [1e6j]

SWISS-PROT database: [P04585] [Q99LC4]

Domain organization of [POL_HV1H2] [Q99LC4_MOUSE] by SWISSPFAM

Domains found in 1E6J: [IG_like] [IGv ] by SMART

Other resources with information on 1E6J

Community annotation for 1E6J 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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