MolNFT v1 · #121479 · protein
Crystal structure of DR2231_E46A mutant in complex with dumpnpp and manganese
5HWU: “Crystal structure of DR2231_E46A mutant in complex with dumpnpp and manganese”. X-ray diffraction, 2 ligands (DUP, MN), 4 pockets (best druggability 0.64). MolNFT v1 #121479 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5HWU
- Type
- protein
- Length
- 268 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DR2231
- UniProt
- Q9RS96
- Ligands
- DUP, MN
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DR2231 | protein | 137 | 63% helix, 1% strand | Q9RS96 |
| B | DR2231 | protein | 131 | 67% helix, 0% strand | Q9RS96 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, B
- MN · Manganese (II) ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.64 | 0.82 | 37 | DUP, MN |
| 2 | 133 | 0.38 | 0.73 | 23 | GOL |
| 3 | 80 | 0.37 | 0.77 | 18 | empty |
| 4 | 71 | 0.34 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3009 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5HWU · Crystal Structure of DR2231_E46A mutant in complex with dUMPNPP and Manganese · 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 5HWU · PDBe 5HWU · UniProt Q9RS96
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