MolNFT v1 · #121425 · protein
Crystal structure of DR2231 in complex with dumpnpp and magnesium.
5HVA: “Crystal structure of DR2231 in complex with dumpnpp and magnesium.”. X-ray diffraction, 2 ligands (DUP, MG), 7 pockets (best druggability 0.81). MolNFT v1 #121425 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HVA
- Type
- protein
- Length
- 540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DR2231
- UniProt
- Q9RS96
- Ligands
- DUP, MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DR2231 | protein | 140 | 62% helix, 1% strand | Q9RS96 |
| B | DR2231 | protein | 139 | 61% helix, 1% strand | Q9RS96 |
| C | DR2231 | protein | 131 | 67% helix, 0% strand | Q9RS96 |
| D | DR2231 | protein | 130 | 68% 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 · 6 copies · chains A, B, C, D
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 | 921 | 0.81 | 0.83 | 104 | DUP, MG |
| 2 | 98 | 0.40 | 0.77 | 17 | empty |
| 3 | 70 | 0.37 | 0.78 | 16 | empty |
| 4 | 71 | 0.37 | 0.78 | 16 | empty |
| 5 | 73 | 0.35 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3072 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 3040 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 201 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 160 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 149 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5HVA · Crystal structure of DR2231 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 5HVA · PDBe 5HVA · UniProt Q9RS96
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