Research workbench
Crystal structure of the E. COLI pyrimidine nucleoside hydrolase yeik (apo-form)
Analyse Crystal structure of the E. COLI pyrimidine nucleoside hydrolase yeik (apo-form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MKM
- Type
- protein
- Length
- 1,217 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
- CA
- Pockets
- 9 · best druggability 0.69
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 | 311 | 43% helix, 18% strand | C3T3U2 |
| B | Putative uncharacterized protein yeik (EC 3.2.2.8) | protein | 302 | 38% helix, 19% strand | C3T3U2 |
| C | Putative uncharacterized protein yeik (EC 3.2.2.8) | protein | 295 | 38% helix, 19% strand | C3T3U2 |
| D | Putative uncharacterized protein yeik (EC 3.2.2.8) | protein | 309 | 42% helix, 18% strand | C3T3U2 |
Ligands and binding sites
- 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.97 | 19 | empty |
| 2 | 179 | 0.64 | 0.85 | 38 | empty |
| 3 | 274 | 0.57 | 0.78 | 31 | empty |
| 4 | 291 | 0.54 | 0.75 | 33 | CA |
| 5 | 229 | 0.52 | 0.76 | 31 | empty |
Interfaces
6 interfaces between chains.
- B–D · 894 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 879 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 834 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 822 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3MKM · Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form) · 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 3MKM · PDBe 3MKM · UniProt C3T3U2
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