OCA Atlas for 1EHL

1EHL

Immune System

date

Feb 21, 2000

title

64m-2 Antibody Fab Complexed With D(5ht)(6-4)T

authors

H.Yokoyama, R.Mizutani, Y.Satow, Y.Komatsu, E.Ohtsuka, O.Nikaido

compound

source

Molecule: 5'-(D(5ht)P(6-4)T)-3'
Chain: A
Engineered: Yes
Other_details: Complex Involves A C6-C4 Bond Between 5ht(1) And T(2), A Photoproduct Ligand;

Synthetic: Yes
Other_details: Purified From Ultraviolet-Radiated Dtpt

Molecule: Anti-(6-4) Photoproduct Antibody 64m-2 Fab (Light Chain);
Chain: L

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: Balbc
Cell_line: Hybridoma

Molecule: Anti-(6-4) Photoproduct Antibody 64m-2 Fab (Heavy Chain);
Chain: H

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: Balbc
Cell_line: Hybridoma

symmetry

Space Group: C 1 2 1

R_factor

0.192

R_Free

0.279

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
144.500	48.062	77.939	90.00	104.69	90.00

method

X-Ray Diffraction

resolution

2.40 Å

ligand

5HT

enzyme

related structures

by homologous chain: 1C5D, 1MRC, 1NGQ

Gene
Ontology

Chain	Function	Process	Component
L

Primary reference

Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation., Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka E, Nikaido O, J Mol Biol 2000 Jun 9;299(3):711-23. PMID:10835279

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]

Biological Unit Coordinates (1ehl.pdb1.gz) 77 Kb

LPC: Ligand-Protein Contacts for 1EHL

CSU: Contacts of Structural Units for 1EHL

Likely Quarternary Molecular Structure file(s) for 1EHL

Structure Factors (129 Kb)

Retrieve 1EHL in mmCIF format [Save to disk]

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

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

View 1EHL 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 1EHL

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 1EHL, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1ehlh1, region H:1-113 [Jmol] [rasmolscript] [script source]
- Domain d1ehlh2, region H:114-227 [Jmol] [rasmolscript] [script source]
- Domain d1ehll1, region L:1-107 [Jmol] [rasmolscript] [script source]
- Domain d1ehll2, region L:108-213 [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: [1ehl_H] [1ehl_A] [1ehl_L] [1ehl]

SWISS-PROT database: [P01863]

Domain organization of [GCAA_MOUSE] by SWISSPFAM

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

Other resources with information on 1EHL

Community annotation for 1EHL 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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