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Crystal structure of rcl with phospho-triciribine
Analyse Crystal structure of rcl with phospho-triciribine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FYH
- Type
- protein
- Length
- 509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribonucleoside 5'-monophosphate N-glycosidase
- EC
- 3.2.2.-
- UniProt
- O35820
- Ligands
- TR5, SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribonucleoside 5'-monophosphate N-glycosidase (EC 3.2.2.-) | protein | 127 | 44% helix, 17% strand | O35820 |
| B, C | Deoxyribonucleoside 5'-monophosphate N-glycosidase (EC 3.2.2.-) | protein | 125 | 45% helix, 18% strand | O35820 |
| D | Deoxyribonucleoside 5'-monophosphate N-glycosidase (EC 3.2.2.-) | protein | 132 | 46% helix, 17% strand | O35820 |
Ligands and binding sites
- TR5 · 5-methyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1,5-dihydro-1,4,5,6,8-pentaazaacenaphthylen-3-amine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.61 | 0.83 | 27 | empty |
| 2 | 202 | 0.58 | 0.80 | 36 | TR5 |
| 3 | 193 | 0.56 | 0.80 | 33 | TR5 |
| 4 | 167 | 0.54 | 0.80 | 32 | TR5 |
| 5 | 84 | 0.53 | 0.85 | 19 | TR5 |
Interfaces
3 interfaces between chains.
- C–D · 1459 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1431 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 410 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 O35820
- Elsewhere: RCSB PDB 4FYH · PDBe 4FYH · UniProt O35820
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