MolNFT v1 · #121540 · protein
Crystal structure of DR2231_E47A mutant in complex with dumpnpp and magnesium
5HYL: “Crystal structure of DR2231_E47A mutant in complex with dumpnpp and magnesium”. X-ray diffraction, 2 ligands (DUP, MG), 8 pockets (best druggability 0.82). MolNFT v1 #121540 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5HYL
- Type
- protein
- Length
- 566 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DR2231
- UniProt
- Q9RS96
- Ligands
- DUP, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DR2231 | protein | 139 | 62% helix, 1% strand | Q9RS96 |
| C | DR2231 | protein | 144 | 62% helix, 0% strand | Q9RS96 |
| D | DR2231 | protein | 144 | 63% helix, 0% strand | Q9RS96 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 2 copies · chains A, C, D, B
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.82 | 0.83 | 97 | DUP, MG |
| 2 | 97 | 0.41 | 0.77 | 22 | empty |
| 3 | 137 | 0.40 | 0.74 | 26 | empty |
| 4 | 87 | 0.40 | 0.78 | 16 | empty |
| 5 | 133 | 0.38 | 0.73 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3066 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 3049 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 199 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 123 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5HYL · Crystal structure of DR2231_E47A mutant in complex with dUMPNPP and magnesium · 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 Q9RS96
- Elsewhere: RCSB PDB 5HYL · PDBe 5HYL · UniProt Q9RS96
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