MolNFT v1 · #111100 · protein
Vaccinia virus his-D4/A20(1-50) in complex with uracil
4YGM · Uracil-DNA glycosylase: “Vaccinia virus his-D4/A20(1-50) in complex with uracil”. X-ray diffraction, 2 ligands (URA, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #111100 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4YGM
- Type
- protein
- Length
- 539 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase; DNA polymerase processivity factor component A20
- EC
- 3.2.2.27
- UniProt
- P20536, P20995
- Ligands
- URA, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 218 | 40% helix, 17% strand | P20536 |
| D | DNA polymerase processivity factor component A20 | protein | 50 | 68% helix, 0% strand | P20995 |
| A | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 220 | 40% helix, 18% strand | P20536 |
| C | DNA polymerase processivity factor component A20 | protein | 51 | 67% helix, 0% strand | P20995 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.69 | 0.77 | 72 | empty |
| 2 | 112 | 0.48 | 0.80 | 27 | SO4, URA |
| 3 | 69 | 0.46 | 0.83 | 15 | SO4, URA |
Interfaces
3 interfaces between chains.
- B–D · 1001 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 957 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 500 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4YGM · Vaccinia virus his-D4/A20(1-50) in complex with uracil · the same entry in another collection · chain B against B, 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 P20536
- Every structure of UniProt P20995
- Elsewhere: RCSB PDB 4YGM · PDBe 4YGM · UniProt P20536 · UniProt P20995
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