Research workbench
Plant nucleoside hydrolase - ZMNRH2B with a bound adenine
Analyse Plant nucleoside hydrolase - ZMNRH2B with a bound adenine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZK4
- Type
- protein
- Length
- 1,266 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine-specific ribonucleoside hydrolase riha
- UniProt
- B6THD4
- Ligands
- ADE, CA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 316 | 39% helix, 19% strand | B6THD4 |
| B, C | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 317 | 38% helix, 19% strand | B6THD4 |
Ligands and binding sites
- ADE · Adenine · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.80 | 0.84 | 83 | ADE |
| 2 | 484 | 0.80 | 0.87 | 66 | CA, ADE |
| 3 | 822 | 0.79 | 0.82 | 87 | ADE |
| 4 | 562 | 0.75 | 0.83 | 62 | ADE |
| 5 | 835 | 0.75 | 0.79 | 63 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1501 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1439 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 547 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 458 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZK4 · Plant nucleoside hydrolase - ZmNRh2b with a bound adenine · 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 6ZK4 · PDBe 6ZK4 · UniProt B6THD4
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