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Crystal structure of wild type LFA1 I domain

Analyse Crystal structure of wild type LFA1 I domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3F74
Type: protein
Length: 540 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin alpha-L
UniProt: P20701
Ligands: MG
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Integrin alpha-L	protein	180	41% helix, 23% strand	P20701

Ligands and binding sites

MG · Magnesium ion · metal · chains C
GOL · Glycerol · additive · 2 copies · chains B

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

Pockets

3 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	1124	0.73	0.76	69	empty
2	294	0.56	0.76	27	empty
3	114	0.38	0.74	18	empty

Interfaces

3 interfaces between chains.

A–B · 549 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 261 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 96 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3F74 · Crystal structure of wild type LFA1 I domain · the same entry in another collection · chain A against A, TM-score 1.00
P20701 · AlphaFold monomer V2.0 prediction for integrin alpha-L (P20701) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P20701
Elsewhere: RCSB PDB 3F74 · PDBe 3F74 · UniProt P20701

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