Research workbench
N4 mini-vrnap transcription initiation complex, 4 min after soaking GTP, ATP and mn
Analyse N4 mini-vrnap transcription initiation complex, 4 min after soaking GTP, ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FF4
- 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
- AMP, POP, 5GP, MN, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Virion RNA polymerase | protein | 1095 | 56% helix, 11% strand | Q859P9 |
| C, D | Bacteriophage N4 P2 promoter | dna | 20 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, C
- POP · Pyrophosphate 2- · ligand · chains A
- 5GP · Guanosine-5'-monophosphate · ligand · chains A, C
- MN · Manganese (II) ion · metal · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.84 | 0.88 | 82 | empty |
| 2 | 1191 | 0.84 | 0.85 | 108 | empty |
| 3 | 1138 | 0.76 | 0.79 | 86 | empty |
| 4 | 810 | 0.74 | 0.79 | 103 | AMP, POP, MN, PO4, 5GP |
| 5 | 633 | 0.71 | 0.79 | 64 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2015 Ų buried · 34 hydrogen bonds · protein-nucleic
- B–D · 1988 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–B · 930 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4FF4 · N4 mini-vRNAP transcription initiation complex, 4 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 4FF4 · PDBe 4FF4 · UniProt Q859P9
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