MolNFT v1 · #52718 · protein
Structure of the discoidin I from dictyostelium discoideum in complex with galnac at 1.75 ångström resolution
2W95 · Discoidin-1 subunit a: “Structure of the discoidin I from dictyostelium discoideum in complex with galnac at 1.75 ångström resolution”. X-ray diffraction, 4 ligands (NGA, CA, NI), 4 pockets (best druggability 0.78). MolNFT v1 #52718…
- PDB
- 2W95
- 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
- NGA, CA, NI, SO4
- Pockets
- 4 · best druggability 0.78
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
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, C, B
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · chains A, B, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, C, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.78 | 0.89 | 66 | empty |
| 2 | 221 | 0.63 | 0.82 | 57 | MPD |
| 3 | 145 | 0.43 | 0.75 | 24 | MRD |
| 4 | 129 | 0.39 | 0.74 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2222 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 2212 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 2207 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 2W95 · STructure of the Discoidin I from Dictyostelium discoideum in complex with GalNAc at 1.75… · 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 C 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 2W95 · PDBe 2W95 · UniProt P02886
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