Research workbench
Plant nucleoside hydrolase - ZMNRH2B in complex with forodesine
Analyse Plant nucleoside hydrolase - ZMNRH2B 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
- 6ZK2
- Type
- protein
- Length
- 1,264 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine-specific ribonucleoside hydrolase riha
- UniProt
- B6THD4
- Ligands
- IMH, CA
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyrimidine-specific ribonucleoside hydrolase riha | protein | 316 | 39% helix, 19% strand | B6THD4 |
Ligands and binding sites
- IMH · 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 12 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, D
- PGE · Triethylene glycol · additive · 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 | 816 | 0.78 | 0.81 | 87 | CA, IMH, DMS, EDO |
| 2 | 523 | 0.78 | 0.85 | 65 | IMH, EDO |
| 3 | 583 | 0.78 | 0.84 | 86 | CA, IMH, DMS, EDO |
| 4 | 752 | 0.76 | 0.81 | 69 | DMS |
| 5 | 516 | 0.74 | 0.82 | 65 | CA, IMH, DMS, EDO |
Interfaces
5 interfaces between chains.
- C–D · 1514 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1488 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 524 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 448 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 94 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZK2 · Plant nucleoside hydrolase - ZmNRh2b 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 B6THD4
- Elsewhere: RCSB PDB 6ZK2 · PDBe 6ZK2 · UniProt B6THD4
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