Research workbench
Structure of D13, the scaffolding protein of vaccinia virus (mutant D513G)
Analyse Structure of D13, the scaffolding protein of vaccinia virus (mutant D513G) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SAM
- Type
- protein
- Length
- 1,627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rifampicin resistance protein
- UniProt
- P68440
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rifampicin resistance protein | protein | 541 | 17% helix, 40% strand | P68440 |
| B | Rifampicin resistance protein | protein | 544 | 17% helix, 40% strand | P68440 |
| C | Rifampicin resistance protein | protein | 542 | 15% helix, 40% strand | P68440 |
Ligands and binding sites
- FMT · Formic acid · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.84 | 0.85 | 106 | empty |
| 2 | 1051 | 0.84 | 0.85 | 98 | FMT |
| 3 | 1066 | 0.84 | 0.85 | 107 | FMT |
| 4 | 374 | 0.59 | 0.76 | 48 | empty |
| 5 | 140 | 0.50 | 0.80 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3217 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3006 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2825 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3SAM · Structure of D13, the scaffolding protein of vaccinia virus (mutant D513G) · 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 P68440
- Elsewhere: RCSB PDB 3SAM · PDBe 3SAM · UniProt P68440
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.