MolNFT v1 · #71656 · protein
Crystal structure of the E. COLI pyrimidine nucleosidase yeik bound to a competitive inhibitor
3MKN · Putative uncharacterized protein yeik: “Crystal structure of the E. COLI pyrimidine nucleosidase yeik bound to a competitive inhibitor”. X-ray diffraction, 2 ligands (DNB, CA), 10 pockets (best druggability 0.65). MolNFT v1 #71656…
- PDB
- 3MKN
- Type
- protein
- Length
- 1,199 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein yeik
- EC
- 3.2.2.8
- UniProt
- C3T3U2
- Ligands
- DNB, CA
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein yeik (EC 3.2.2.8) | protein | 303 | 41% helix, 18% strand | C3T3U2 |
| B | Putative uncharacterized protein yeik (EC 3.2.2.8) | protein | 301 | 40% helix, 19% strand | C3T3U2 |
| C | Putative uncharacterized protein yeik (EC 3.2.2.8) | protein | 292 | 39% helix, 19% strand | C3T3U2 |
| D | Putative uncharacterized protein yeik (EC 3.2.2.8) | protein | 303 | 40% helix, 19% strand | C3T3U2 |
Ligands and binding sites
- DNB · (2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.65 | 0.84 | 31 | DNB |
| 2 | 343 | 0.64 | 0.79 | 46 | DNB |
| 3 | 418 | 0.64 | 0.78 | 36 | CA, DNB |
| 4 | 192 | 0.50 | 0.76 | 33 | empty |
| 5 | 214 | 0.50 | 0.76 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 876 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 876 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 832 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 817 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3MKN · Crystal structure of the E. coli pyrimidine nucleosidase YeiK bound to a competitive… · the same entry in another collection · chain A against A, TM-score 1.00
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 C3T3U2
- Elsewhere: RCSB PDB 3MKN · PDBe 3MKN · UniProt C3T3U2
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