MolNFT v1 · #171890 · protein
Plant nucleoside hydrolase - ZMNRH2B in complex with ribose
6ZK3 · Pyrimidine-specific ribonucleoside hydrolase riha: “Plant nucleoside hydrolase - ZMNRH2B in complex with ribose”. X-ray diffraction, 2 ligands (RIB, CA), 14 pockets (best druggability 0.78). MolNFT v1 #171890 on GenesisL1: 3D…
- PDB
- 6ZK3
- Type
- protein
- Length
- 1,905 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine-specific ribonucleoside hydrolase riha
- UniProt
- B6THD4
- Ligands
- RIB, CA
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 319 | 38% helix, 19% strand | B6THD4 |
| B, C | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 318 | 38% helix, 19% strand | B6THD4 |
| D, F | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 317 | 39% helix, 19% strand | B6THD4 |
| E | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 316 | 39% helix, 19% strand | B6THD4 |
Ligands and binding sites
- RIB · alpha-D-ribofuranose · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 14 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 12 copies · chains A, C, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.78 | 0.80 | 106 | PGE, CA, RIB |
| 2 | 519 | 0.74 | 0.82 | 59 | RIB, EDO |
| 3 | 488 | 0.73 | 0.82 | 59 | RIB, EDO |
| 4 | 534 | 0.73 | 0.81 | 60 | CA, RIB, EDO |
| 5 | 296 | 0.71 | 0.85 | 52 | CA, RIB, PGE |
Interfaces
6 interfaces between chains.
- E–F · 1556 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1466 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 430 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 278 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6ZK3 · Plant nucleoside hydrolase - ZmNRh2b in complex with ribose · 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 6ZK3 · PDBe 6ZK3 · UniProt B6THD4
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