MolNFT v1 · #4819 · protein

Integrin ALPHA2 I domain / collagen complex

1DZI: “Integrin ALPHA2 I domain / collagen complex”. X-ray diffraction, 2 ligands (CO, NH2), 2 pockets (best druggability 0.47). MolNFT v1 #4819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DZI
Type: protein
Length: 248 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin; Collagen
UniProt: P17301
Ligands: CO, NH2
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrin	protein	185	40% helix, 21% strand	P17301
B, C, D	Collagen	protein	21	0% helix, 0% strand	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · chains A, 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	196	0.47	0.75	29	empty
2	70	0.36	0.76	14	empty

Interfaces

6 interfaces between chains.

B–C · 698 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 617 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 601 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 408 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 298 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (hydroxylation).

Compared structures

1DZI · integrin alpha2 I domain / collagen complex · the same entry in another collection · chain A against A, TM-score 1.00
P17301 · AlphaFold monomer V2.0 prediction for integrin alpha-2 (P17301) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P17301
Elsewhere: RCSB PDB 1DZI · PDBe 1DZI · UniProt P17301

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