MolNFT v1 · #171888 · protein
Plant nucleoside hydrolase - ZMNRH2B enzyme
6ZK1 · Pyrimidine-specific ribonucleoside hydrolase riha: “Plant nucleoside hydrolase - ZMNRH2B enzyme”. X-ray diffraction, 2 ligands (CA, CL), 10 pockets (best druggability 0.80). MolNFT v1 #171888 on GenesisL1: 3D structure, binding…
- PDB
- 6ZK1
- Type
- protein
- Length
- 1,265 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine-specific ribonucleoside hydrolase riha
- UniProt
- B6THD4
- Ligands
- CA, CL
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 316 | 39% helix, 18% strand | B6THD4 |
| B | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 317 | 38% helix, 19% strand | B6THD4 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, A, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.80 | 0.84 | 84 | CA, EDO |
| 2 | 624 | 0.78 | 0.83 | 79 | CA, GOL, EDO, CL |
| 3 | 465 | 0.78 | 0.86 | 64 | CA, EDO |
| 4 | 581 | 0.76 | 0.83 | 60 | EDO |
| 5 | 503 | 0.73 | 0.82 | 58 | EDO, CA |
Interfaces
5 interfaces between chains.
- C–D · 1452 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1450 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 478 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 80 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ZK1 · Plant nucleoside hydrolase - ZmNRh2b enzyme · 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 B6THD4
- Elsewhere: RCSB PDB 6ZK1 · PDBe 6ZK1 · UniProt B6THD4
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