Research workbench
Human dutpase in complex with ALPHA,BETA-imido-dutp and MG2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site
Analyse Human dutpase in complex with ALPHA,BETA-imido-dutp and MG2+: visualization of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EHW
- Type
- protein
- Length
- 841 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutp pyrophosphatase
- EC
- 3.6.1.23
- UniProt
- Q6FHN1
- Ligands
- DUP, MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dutp pyrophosphatase (EC 3.6.1.23) | protein | 141 | 5% helix, 43% strand | Q6FHN1 |
| B, C, X, Y, Z | Dutp pyrophosphatase (EC 3.6.1.23) | protein | 140 | 5% helix, 44% strand | Q6FHN1 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 6 copies · chains A, B, C, X, Y, Z
- MG · Magnesium ion · metal · 8 copies · chains A, C, B, X, Z, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.79 | 0.98 | 27 | empty |
| 2 | 110 | 0.78 | 0.98 | 28 | empty |
| 3 | 117 | 0.77 | 0.97 | 30 | DUP, MG |
| 4 | 108 | 0.76 | 0.96 | 28 | DUP, MG |
| 5 | 106 | 0.76 | 0.96 | 33 | DUP, MG |
Interfaces
11 interfaces between chains.
- A–B · 2432 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 2416 Ų buried · 43 hydrogen bonds · protein-protein
- X–Y · 2391 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2364 Ų buried · 48 hydrogen bonds · protein-protein
- X–Z · 2332 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 3EHW · Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the… · 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 Q6FHN1
- Elsewhere: RCSB PDB 3EHW · PDBe 3EHW · UniProt Q6FHN1
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