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)

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)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13591
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B]	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		Interactions Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain G [auth B] Focus chain J [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	E [auth B], F [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	D [auth A], H [auth B], K [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

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

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Help and Resources

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

2E3V | pdb_00002e3v