MolNFT v1 · #28979 · protein
The crystal structure of the PSI/HYBRID domain/ I-EGF1 segment from the human integrin BETA2 at 1.8 resolution
1YUK · Integrin beta-2 a chain: “The crystal structure of the PSI/HYBRID domain/ I-EGF1 segment from the human integrin BETA2 at 1.8 resolution”. X-ray diffraction, 1 ligand (NDG), 1 pocket (best druggability 0.39). MolNFT v1 #28979 on…
- PDB
- 1YUK
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin beta-2 a chain; Integrin beta-2 B chain
- UniProt
- P05107
- Ligands
- NDG
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin beta-2 a chain | protein | 94 | 19% helix, 29% strand | P05107 |
| B | Integrin beta-2 B chain | protein | 120 | 6% helix, 45% strand | P05107 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.39 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1975 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1YUK · The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin… · the same entry in another collection · chain A against A, TM-score 1.00
- P05107 · AlphaFold monomer V2.0 prediction for integrin beta-2 (P05107) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P05107
- Elsewhere: RCSB PDB 1YUK · PDBe 1YUK · UniProt P05107
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