MolNFT v1 · #52717 · protein
Native structure of the discoidin I from dictyostelium discoideum at 1.8 ångström resolution
2W94 · Discoidin-1 subunit a: “Native structure of the discoidin I from dictyostelium discoideum at 1.8 ångström resolution”. X-ray diffraction, 3 ligands (CA, NI, SO4), 8 pockets (best druggability 0.75). MolNFT v1 #52717 on GenesisL1: 3D…
- PDB
- 2W94
- Type
- protein
- Length
- 760 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Discoidin-1 subunit a
- UniProt
- P02886
- Ligands
- CA, NI, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Discoidin-1 subunit a | protein | 254 | 6% helix, 52% strand | P02886 |
| B, C | Discoidin-1 subunit a | protein | 253 | 5% helix, 52% strand | P02886 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, C, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.75 | 0.89 | 52 | empty |
| 2 | 174 | 0.68 | 0.87 | 56 | empty |
| 3 | 79 | 0.57 | 0.87 | 20 | empty |
| 4 | 66 | 0.33 | 0.75 | 14 | empty |
| 5 | 74 | 0.32 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2215 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2214 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 2206 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 2W94 · Native structure of the Discoidin I from Dictyostelium discoideum at 1.8 angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
- P02886 · AlphaFold monomer V2.0 prediction for discoidin-1 subunit a (P02886) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 P02886
- Elsewhere: RCSB PDB 2W94 · PDBe 2W94 · UniProt P02886
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