MolNFT v1 · #121610 · protein
Crystal structure of DR2231_E47A mutant in complex with dump
5I0J: “Crystal structure of DR2231_E47A mutant in complex with dump”. X-ray diffraction, 1 ligand (UMP), 7 pockets (best druggability 0.82). MolNFT v1 #121610 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I0J
- Type
- protein
- Length
- 542 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DR2231
- UniProt
- Q9RS96
- Ligands
- UMP
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DR2231 | protein | 140 | 62% helix, 1% strand | Q9RS96 |
| B | DR2231 | protein | 138 | 63% helix, 1% strand | Q9RS96 |
| C | DR2231 | protein | 132 | 67% helix, 0% strand | Q9RS96 |
| D | DR2231 | protein | 132 | 68% helix, 0% strand | Q9RS96 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.82 | 0.83 | 101 | UMP |
| 2 | 162 | 0.43 | 0.74 | 25 | empty |
| 3 | 94 | 0.39 | 0.77 | 20 | empty |
| 4 | 82 | 0.38 | 0.77 | 19 | empty |
| 5 | 83 | 0.38 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3043 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 3023 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 201 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 128 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 125 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5I0J · Crystal structure of DR2231_E47A mutant in complex with dUMP · 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 5I0J · PDBe 5I0J · UniProt Q9RS96
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