Research workbench
Structure of EMS16-ALPHA2-I domain complex
Analyse Structure of EMS16-ALPHA2-I domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V7P
- Type
- protein
- Length
- 454 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EMS16 a chain; EMS16 B chain; Integrin alpha-2
- UniProt
- Q7T2Q1, Q7T2Q0, P17301
- Ligands
- NAG, MN, PO4, CL
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EMS16 a chain | protein | 134 | 22% helix, 31% strand | Q7T2Q1 |
| B | EMS16 B chain | protein | 127 | 20% helix, 37% strand | Q7T2Q0 |
| C | Integrin alpha-2 | protein | 193 | 44% helix, 22% strand | P17301 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- MN · Manganese (II) ion · metal · chains C
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.72 | 0.82 | 52 | MN |
Interfaces
3 interfaces between chains.
- A–B · 1917 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 670 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 388 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1V7P · Structure of EMS16-alpha2-I domain 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 C against A, TM-score 0.99
- Q7T2Q0 · AlphaFold monomer V2.0 prediction for snaclec EMS16 subunit beta (Q7T2Q0) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q7T2Q1 · AlphaFold monomer V2.0 prediction for snaclec EMS16 subunit alpha (Q7T2Q1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q7T2Q1
- Every structure of UniProt Q7T2Q0
- Every structure of UniProt P17301
- Elsewhere: RCSB PDB 1V7P · PDBe 1V7P · UniProt Q7T2Q1 · UniProt Q7T2Q0 · UniProt P17301
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.