MolNFT v1 · #55960 · protein
Crystal structure of EBV-DNA polymerase accessory protein BMRF1
2Z0L · Early antigen protein D: “Crystal structure of EBV-DNA polymerase accessory protein BMRF1”. X-ray diffraction, 1 ligand (CL), 16 pockets (best druggability 0.71). MolNFT v1 #55960 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2Z0L
- Type
- protein
- Length
- 2,392 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Early antigen protein D
- UniProt
- P03191
- Ligands
- CL
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Early antigen protein D | protein | 299 | 19% helix, 42% strand | P03191 |
Ligands and binding sites
- CL · Chloride ion · ion · 9 copies · chains A, C, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.71 | 0.77 | 86 | empty |
| 2 | 603 | 0.68 | 0.77 | 66 | empty |
| 3 | 438 | 0.62 | 0.77 | 48 | empty |
| 4 | 360 | 0.61 | 0.78 | 35 | empty |
| 5 | 376 | 0.61 | 0.77 | 46 | empty |
Interfaces
8 interfaces between chains.
- G–H · 961 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 958 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 937 Ų buried · 17 hydrogen bonds · protein-protein
- B–G · 613 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 502 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 2Z0L · Crystal structure of EBV-DNA polymerase accessory protein BMRF1 · 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 P03191
- Elsewhere: RCSB PDB 2Z0L · PDBe 2Z0L · UniProt P03191
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