Research workbench
Plant nucleoside hydrolase - ZMNRH3 enzyme in complex with forodesine
Analyse Plant nucleoside hydrolase - ZMNRH3 enzyme in complex with forodesine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZK5
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside N-ribohydrolase 3
- EC
- 3.2.2.-
- UniProt
- B6T563
- Ligands
- IMH, CA
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside N-ribohydrolase 3 (EC 3.2.2.-) | protein | 316 | 39% helix, 19% strand | B6T563 |
Ligands and binding sites
- IMH · 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.71 | 0.83 | 54 | CA, IMH |
| 2 | 321 | 0.69 | 0.83 | 50 | IMH, CA |
| 3 | 52 | 0.66 | 0.95 | 16 | empty |
| 4 | 61 | 0.66 | 0.93 | 16 | empty |
| 5 | 129 | 0.49 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1490 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6ZK5 · Plant nucleoside hydrolase - ZmNRh3 enzyme in complex with forodesine · 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 B6T563
- Elsewhere: RCSB PDB 6ZK5 · PDBe 6ZK5 · UniProt B6T563
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.