MolNFT v1 · #102153 · protein
Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20 N-terminus
4ODA · Uracil-DNA glycosylase: “Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20…”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.70). MolNFT v1 #102153 on GenesisL1…
- PDB
- 4ODA
- Type
- protein
- Length
- 543 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
- SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 221 | 39% helix, 17% strand | P20536 |
| D, C | DNA polymerase processivity factor component A20 | protein | 51 | 67% helix, 0% strand | P20995 |
| A | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 220 | 38% helix, 18% strand | P20536 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.70 | 0.77 | 75 | empty |
| 2 | 78 | 0.51 | 0.84 | 18 | SO4, GOL |
| 3 | 72 | 0.45 | 0.81 | 17 | SO4, GOL |
Interfaces
3 interfaces between chains.
- B–D · 976 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 954 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 528 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4ODA · Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex… · 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 4ODA · PDBe 4ODA · UniProt P20536 · UniProt P20995
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