Research workbench

Alpha-1 integrin I-domain in complex with glogen triple helical peptide

Analyse Alpha-1 integrin I-domain in complex with glogen triple helical peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2M32
Type: protein
Length: 255 residues
Chains: 4
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin alpha-1; Glogen peptide
UniProt: P56199
Ligands: ACE, MG, NH2
Pockets: 2 · best druggability 0.48

Structure

solution nmr · 2 distinct chains · 34% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrin alpha-1	protein	192	38% helix, 17% strand	P56199
B, C, D	Glogen peptide	protein	21	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 3 copies · chains B, C, D
MG · Magnesium ion · metal · chains A, B, C
NH2 · Amino group · ion · 3 copies · chains B, C, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.48	0.81	18	empty
2	83	0.36	0.76	19	empty

Interfaces

6 interfaces between chains.

C–D · 659 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 650 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 632 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 369 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 363 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified, 3 covalent (hydroxylation, covalent ligand).

Compared structures

2M32 · Alpha-1 integrin I-domain in complex with GLOGEN triple helical peptide · the same entry in another collection · chain A against A, TM-score 1.00
P56199 · AlphaFold monomer V2.0 prediction for integrin alpha-1 (P56199) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P56199
Elsewhere: RCSB PDB 2M32 · PDBe 2M32 · UniProt P56199

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