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Structural plasticity in igsf domain 4 of icam-1 mediates cell surface dimerization

Analyse Structural plasticity in igsf domain 4 of icam-1 mediates cell surface… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OZ4
Type: protein
Length: 687 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Intercellular adhesion molecule 1; Fab fragment light chain; Fab fragment, heavy chain
UniProt: Q5NKV7, Q58EU4, P01757
Ligands: NAG, FUC, ZN, SO4
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Intercellular adhesion molecule 1	protein	265	6% helix, 57% strand	Q5NKV7
L	Fab fragment light chain	protein	214	6% helix, 50% strand	Q58EU4
H	Fab fragment, heavy chain	protein	208	4% helix, 50% strand	P01757

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
FUC · alpha-L-fucopyranose · sugar
ZN · Zinc ion · metal · 2 copies · chains L
SO4 · Sulfate ion · ion · 2 copies · chains A, L
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains L, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	545	0.64	0.76	56	TRS
2	277	0.52	0.75	39	empty
3	165	0.48	0.77	23	empty
4	92	0.43	0.78	15	empty
5	65	0.34	0.76	19	empty

Interfaces

3 interfaces between chains.

L–H · 1820 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 736 Å² buried · 18 hydrogen bonds · protein-protein
A–L · 411 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

2OZ4 · Structural Plasticity in IgSF Domain 4 of ICAM-1 Mediates Cell Surface Dimerization · the same entry in another collection · chain A against A, TM-score 1.00
P01757 · AlphaFold monomer V2.0 prediction for ig heavy chain V region J558 (P01757) · a predicted model of the same protein · chain H against A, TM-score 0.54

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q5NKV7
Every structure of UniProt Q58EU4
Every structure of UniProt P01757
Elsewhere: RCSB PDB 2OZ4 · PDBe 2OZ4 · UniProt Q5NKV7 · UniProt Q58EU4 · UniProt P01757

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