Research workbench
Integrin ALPHA2 I domain E318W-collagen complex
Analyse Integrin ALPHA2 I domain E318W-collagen complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BJ3
- Type
- protein
- Length
- 416 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-2; Gfoger peptide
- UniProt
- P17301
- Ligands
- MG, CL
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-2 | protein | 183 | 36% helix, 21% strand | P17301 |
| B | Integrin alpha-2 | protein | 179 | 34% helix, 20% strand | P17301 |
| C, D, E | Gfoger peptide | protein | 18 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, E, B, C
- CL · Chloride ion · ion · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.64 | 0.76 | 41 | empty |
| 2 | 72 | 0.41 | 0.78 | 16 | empty |
| 3 | 81 | 0.39 | 0.78 | 15 | empty |
| 4 | 86 | 0.36 | 0.75 | 20 | empty |
Interfaces
10 interfaces between chains.
- D–E · 590 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 580 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 527 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 345 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 328 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (hydroxylation).
Compared structures
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 4BJ3 · PDBe 4BJ3 · UniProt P17301
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