Research workbench
Structure of the genome packaging NTPase B204 from sulfolobus turreted icosahedral virus 2 in complex with amppcp
Analyse Structure of the genome packaging NTPase B204 from sulfolobus turreted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KFU
- Type
- protein
- Length
- 791 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome packaging NTPase B204
- EC
- 3.-.-.-
- UniProt
- D5IEZ9
- Ligands
- ACP, MG, ZN
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome packaging NTPase B204 (EC 3.-.-.-) | protein | 205 | 40% helix, 23% strand | D5IEZ9 |
| B | Genome packaging NTPase B204 (EC 3.-.-.-) | protein | 196 | 41% helix, 25% strand | D5IEZ9 |
| C | Genome packaging NTPase B204 (EC 3.-.-.-) | protein | 195 | 42% helix, 24% strand | D5IEZ9 |
| D | Genome packaging NTPase B204 (EC 3.-.-.-) | protein | 195 | 43% helix, 24% strand | D5IEZ9 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 6 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FLC · Citrate anion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.56 | 0.82 | 22 | empty |
| 2 | 242 | 0.53 | 0.76 | 36 | empty |
| 3 | 262 | 0.53 | 0.76 | 32 | ACP, MG |
| 4 | 63 | 0.50 | 0.85 | 16 | empty |
| 5 | 116 | 0.48 | 0.79 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–C · 511 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 456 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 308 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4KFU · Structure of the genome packaging NTPase B204 from Sulfolobus turreted icosahedral virus… · 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 D5IEZ9
- Elsewhere: RCSB PDB 4KFU · PDBe 4KFU · UniProt D5IEZ9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.