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Crystal structure of DDB1 in complex with simian virus 5 V protein
Analyse Crystal structure of DDB1 in complex with simian virus 5 V protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B5L
- Type
- protein
- Length
- 2,615 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Damage-specific DNA binding protein 1; Nonstructural protein V
- UniProt
- P11207
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Damage-specific DNA binding protein 1 | protein | 1132 | 5% helix, 50% strand | — |
| B | Damage-specific DNA binding protein 1 | protein | 1134 | 6% helix, 46% strand | — |
| C | Nonstructural protein V | protein | 174 | 13% helix, 23% strand | P11207 |
| D | Nonstructural protein V | protein | 175 | 12% helix, 22% strand | P11207 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.81 | 0.85 | 89 | empty |
| 2 | 593 | 0.78 | 0.84 | 55 | empty |
| 3 | 943 | 0.77 | 0.80 | 86 | empty |
| 4 | 928 | 0.76 | 0.79 | 75 | empty |
| 5 | 489 | 0.75 | 0.83 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1943 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1867 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 852 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2B5L · Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein · 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 P11207
- Elsewhere: RCSB PDB 2B5L · PDBe 2B5L · UniProt P11207
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