OCA Atlas for 1OAK

1OAK

Complex (Willebrand Immunoglobulin)

date

Dec 18, 1997

title

Crystal Structure Of The Von Willebrand Factor (Vwf) A1 Domain In Complex With The Function Blocking Nmc-4 Fab

authors

R.Celikel, K.I.Varughese

compound

source

Molecule: Nmc-4 Igg1
Chain: L
Fragment: Fab Fragment, An Anti Von Willebrand Factor (Vwf) A1 Domain;
Engineered: Yes
Other_details: The Antibody Heavy Chain Consists Of Two Segments, H1 And H2, Both Labeled Chain H In This Entry;

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Cell_line: Hybridoma
Organ: Blood
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell_line: Mopc21

Molecule: Nmc-4 Igg1
Chain: H
Fragment: Fab Fragment, An Anti Von Willebrand Factor (Vwf) A1 Domain;
Engineered: Yes
Other_details: The Antibody Heavy Chain Consists Of Two Segments, H1 And H2, Both Labeled Chain H In This Entry;

Molecule: Von Willebrand Factor
Chain: A
Fragment: A1 Domain Residues 507 - 702, Or Glycoprotein
Iba (A\: Alpha) Binding Domain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Blood
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: T7 Promoter
Expression_system_plasmid: Pet8c

symmetry

Space Group: C 1 2 1

R_factor

0.201

R_Free

0.274

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
208.200	61.900	72.900	90.00	108.60	90.00

method

X-Ray Diffraction

resolution

2.20 Å

related structures

by homologous chain: 1AUQ, 1FNS, 1KCU, 1YEE, 2CK0, 43C9

Primary reference

Crystal structure of the von Willebrand factor A1 domain in complex with the function blocking NMC-4 Fab., Celikel R, Varughese KI, Madhusudan, Yoshioka A, Ware J, Ruggeri ZM, Nat Struct Biol 1998 Mar;5(3):189-94. PMID:9501911

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]

Biological Unit Coordinates (1oak.pdb1.gz) 108 Kb

CSU: Contacts of Structural Units for 1OAK

Likely Quarternary Molecular Structure file(s) for 1OAK

Retrieve 1OAK in mmCIF format [Save to disk]

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

View 1OAK 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 1OAK

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1OAK, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1oaka_, region A [Jmol] [rasmolscript] [script source]
- Domain d1oakh1, region H:215-336 [Jmol] [rasmolscript] [script source]
- Domain d1oakh2, region H:337-437 [Jmol] [rasmolscript] [script source]
- Domain d1oakl1, region L:1-107 [Jmol] [rasmolscript] [script source]
- Domain d1oakl2, region L:108-212 [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: [1oak_H] [1oak_A] [1oak] [1oak_L]

SWISS-PROT database: [P01837] [P04275]

Domain organization of [IGKC_MOUSE] [VWF_HUMAN] by SWISSPFAM

Domains found in 1OAK: [IG_like] [IGv] [VWA ] by SMART

Other resources with information on 1OAK

Community annotation for 1OAK 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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