Research workbench
Cryo-EM structure of human integrin ALPHA5BETA1 in the half-bent conformation
Analyse Cryo-EM structure of human integrin ALPHA5BETA1 in the half-bent conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NXD
- Type
- protein
- Length
- 1,595 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-5; Integrin beta-1
- UniProt
- P08648, P05556
- Ligands
- NAG, BMA, MAN, CA, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-5 | protein | 905 | 4% helix, 39% strand | P08648 |
| B | Integrin beta-1 | protein | 690 | 19% helix, 20% strand | P05556 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 7 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 7 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.83 | 0.85 | 93 | empty |
| 2 | 1024 | 0.75 | 0.78 | 94 | empty |
| 3 | 778 | 0.68 | 0.75 | 82 | empty |
| 4 | 427 | 0.63 | 0.77 | 40 | empty |
| 5 | 124 | 0.62 | 0.86 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2388 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 7NXD · Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation · the same entry in another collection · chain A against A, TM-score 1.00
- P05556 · AlphaFold monomer V2.0 prediction for integrin beta-1 (P05556) · a predicted model of the same protein · chain B against A, TM-score 0.72
- P08648 · AlphaFold monomer V2.0 prediction for integrin alpha-5 (P08648) · a predicted model of the same protein · chain A against A, TM-score 0.67
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 P08648
- Every structure of UniProt P05556
- Elsewhere: RCSB PDB 7NXD · PDBe 7NXD · UniProt P08648 · UniProt P05556
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