MolNFT v1 · #91498 · protein + DNA
N4 mini-vrnap transcription initiation complex, 3 min after soaking GTP, ATP and mn
4FF3 · Virion RNA polymerase: “N4 mini-vrnap transcription initiation complex, 3 min after soaking GTP, ATP and mn”. X-ray diffraction, 4 ligands (ATP, 5GP, MN), 20 pockets (best druggability 0.86). MolNFT v1 #91498 on GenesisL1: 3D…
- PDB
- 4FF3
- Type
- protein + DNA
- Length
- 2,230 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion RNA polymerase; Bacteriophage N4 P2 promoter
- UniProt
- Q859P9
- Ligands
- ATP, 5GP, MN, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Virion RNA polymerase | protein | 1095 | 57% helix, 11% strand | Q859P9 |
| C, D | Bacteriophage N4 P2 promoter | dna | 20 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, C
- 5GP · Guanosine-5'-monophosphate · ligand · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.86 | 0.87 | 106 | empty |
| 2 | 1097 | 0.85 | 0.87 | 110 | empty |
| 3 | 848 | 0.77 | 0.81 | 77 | empty |
| 4 | 271 | 0.71 | 0.86 | 36 | empty |
| 5 | 348 | 0.67 | 0.81 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2025 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–D · 1995 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–B · 1059 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4FF3 · N4 mini-vRNAP transcription initiation complex, 3 min after soaking GTP, ATP and Mn · 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 Q859P9
- Elsewhere: RCSB PDB 4FF3 · PDBe 4FF3 · UniProt Q859P9
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