251,806
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

3TCX | pdb_00003tcx

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

👁 Image

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
Modeled 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	👁 Image
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

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	👁 Image
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

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 FA [auth H] SDF format, chain GA [auth J] SDF format, chain HA [auth L] SDF format, chain IA [auth N] SDF format, chain MA [auth V] SDF format, chain NA [auth X] SDF format, chain OA [auth Z] SDF format, chain PA [auth b] SDF format, chain LA [auth T] SDF format, chain KA [auth R] SDF format, chain JA [auth P] SDF format, chain EA [auth F] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth D] 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 MA [auth V] MOL2 format, chain NA [auth X] MOL2 format, chain OA [auth Z] MOL2 format, chain PA [auth b] MOL2 format, chain LA [auth T] MOL2 format, chain KA [auth R] MOL2 format, chain JA [auth P] MOL2 format, chain EA [auth F] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth D] 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 MA [auth V] mmCIF format, chain NA [auth X] mmCIF format, chain OA [auth Z] mmCIF format, chain PA [auth b] mmCIF format, chain LA [auth T] mmCIF format, chain KA [auth R] mmCIF format, chain JA [auth P] mmCIF format, chain EA [auth F]	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	👁 Image	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] 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

👁 Image

View more in-depth experimental data

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

RCSB PDB is a member of
👁 wwPDB
👁 EMDataResource

RCSB Partners
Nucleic Acid Knowledgebase

👁 CoreTrustSeal

👁 Global Biodata Coalition Logo

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

URL: https://www.rcsb.org/structure/3TCX

⇱ RCSB PDB - 3TCX: Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain of Native C-Terminal Helix Conformation

3TCX | pdb_00003tcx

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2