3TCX

Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain of Native C-Terminal Helix Conformation

PDB DOI: https://doi.org/10.2210/pdb3TCX/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-08-09 Released: 2011-08-31
Deposition Author(s): Kang, S., Kim, C.U., Gu, X., Owens, R.M., van Rijn, S.J., Boonyaleepun, V., Mao, Y., Springer, T.A., Jin, M.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.234 (Depositor), 0.227 (DCC)
R-Value Work:
0.218 (Depositor), 0.210 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity L Integrin I Domain of Native C-Terminal Helix Conformation

Kang, S., Kim, C.U., Gu, X., Owens, R.M., van Rijn, S.J., Boonyaleepun, V., Mao, Y., Springer, T.A., Jin, M.M.

To be published.

Macromolecule Content

Total Structure Weight: 418.06 kDa
Atom Count: 29,330
Modelled Residue Count: 3,710
Deposited Residue Count: 3,710
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intercellular adhesion molecule 1	A AA [auth a] C E G A, AA [auth a], C, E, G, I, K, M, O, Q, S, U, W, Y	85	Homo sapiens	Mutation(s): 7 Gene Names: ICAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P05362 (Homo sapiens) Explore P05362 Go to UniProtKB: P05362
PHAROS: P05362 GTEx: ENSG00000090339
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05362
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	B BA [auth b] D F H B, BA [auth b], D, F, H, J, L, N, P, R, T, V, X, Z	180	Homo sapiens	Mutation(s): 1 Gene Names: ITGAL, CD11A
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens) Explore P20701 Go to UniProtKB: P20701
PHAROS: P20701 GTEx: ENSG00000005844
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20701
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth D] SDF format, chain EA [auth F] SDF format, chain FA [auth H] SDF format, chain GA [auth J] SDF format, chain HA [auth L] SDF format, chain IA [auth N] SDF format, chain JA [auth P] SDF format, chain KA [auth R] SDF format, chain LA [auth T] SDF format, chain MA [auth V] SDF format, chain NA [auth X] SDF format, chain OA [auth Z] SDF format, chain PA [auth b] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth J] MOL2 format, chain HA [auth L] MOL2 format, chain IA [auth N] MOL2 format, chain JA [auth P] MOL2 format, chain KA [auth R] MOL2 format, chain LA [auth T] MOL2 format, chain MA [auth V] MOL2 format, chain NA [auth X] MOL2 format, chain OA [auth Z] MOL2 format, chain PA [auth b] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth J] mmCIF format, chain HA [auth L] mmCIF format, chain IA [auth N] mmCIF format, chain JA [auth P] mmCIF format, chain KA [auth R] mmCIF format, chain LA [auth T] mmCIF format, chain MA [auth V] mmCIF format, chain NA [auth X] mmCIF format, chain OA [auth Z] mmCIF format, chain PA [auth b]	CA [auth B] DA [auth D] EA [auth F] FA [auth H] GA [auth J] CA [auth B], DA [auth D], EA [auth F], FA [auth H], GA [auth J], HA [auth L], IA [auth N], JA [auth P], KA [auth R], LA [auth T], MA [auth V], NA [auth X], OA [auth Z], PA [auth b]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth D] Focus chain EA [auth F] Focus chain FA [auth H] Focus chain GA [auth J] Focus chain HA [auth L] Focus chain IA [auth N] Focus chain JA [auth P] Focus chain KA [auth R] Focus chain LA [auth T] Focus chain MA [auth V] Focus chain NA [auth X] Focus chain OA [auth Z] Focus chain PA [auth b] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth D] Focus chain EA [auth F] Focus chain FA [auth H] Focus chain GA [auth J] Focus chain HA [auth L] Focus chain IA [auth N] Focus chain JA [auth P] Focus chain KA [auth R] Focus chain LA [auth T] Focus chain MA [auth V] Focus chain NA [auth X] Focus chain OA [auth Z] Focus chain PA [auth b]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.234 (Depositor), 0.227 (DCC)
R-Value Work: 0.218 (Depositor), 0.210 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.041	α = 90
b = 166.334	β = 90
c = 299.372	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2011-09-07
Changes: Other
Version 1.2: 2014-11-12
Changes: Structure summary
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary