2E3V | pdb_00002e3v

Crystal structure of the first fibronectin type III domain of neural cell adhesion molecule splicing isoform from human muscle culture lambda-4.4

• PDB DOI: https://doi.org/10.2210/pdb2E3V/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2006-11-30 Released: 2007-06-05 
• Deposition Author(s): Nishino, A., Saijo, S., Kishishita, S., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.211 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Crystal structure of the first fibronectin type III domain of neural cell adhesion molecule splicing isoform from human muscle culture lambda-4.4

Saijo, S., Nishino, A., Kishishita, S., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.63 kDa 
• Atom Count: 2,587 
• Modeled Residue Count: 301 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neural cell adhesion molecule 1, 140 kDa isoform	A, B, C	122	Homo sapiens	Mutation(s): 0  Gene Names: NCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P13591 (Homo sapiens) Explore P13591  Go to UniProtKB:  P13591
PHAROS:  P13591 GTEx:  ENSG00000149294

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	G [auth B], J [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
PGE	E [auth B], F [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth A], H [auth B], K [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.211 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.378	α = 90
b = 55.378	β = 90
c = 118.83	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Nishino, A., Saijo, S., Kishishita, S., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-06-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary