MolNFT v1 · #127869 · protein + DNA + RNA
Tfiiib -TBP/BRF2/DNA and sant domain of BDP1-
5N9G · Transcription factor iiib 50 kda subunit: “Tfiiib -TBP/BRF2/DNA and sant domain of BDP1-”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.81). MolNFT v1 #127869 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N9G
- Type
- protein + DNA + RNA
- Length
- 1,251 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor iiib 50 kda subunit; Tata-box-binding protein; Transcription factor…
- UniProt
- Q9HAW0, P20226, A6H8Y1
- Ligands
- NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor iiib 50 kda subunit | protein | 307 | 61% helix, 1% strand | Q9HAW0 |
| B, G | Tata-box-binding protein | protein | 178 | 26% helix, 38% strand | P20226 |
| C | Transcription factor tfiiib component B'' homolog | protein | 97 | 63% helix, 0% strand | A6H8Y1 |
| D, I | DNA/RNA (27-mer) | dna | 27 | — | — |
| E, J | DNA/RNA (25-mer) | rna | 25 | — | — |
| F | Transcription factor iiib 50 kda subunit | protein | 289 | 65% helix, 1% strand | Q9HAW0 |
| H | Transcription factor tfiiib component B'' homolog | protein | 98 | 64% helix, 0% strand | A6H8Y1 |
Ligands and binding sites
- NA · Sodium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.81 | 0.83 | 77 | empty |
| 2 | 795 | 0.75 | 0.80 | 38 | empty |
| 3 | 673 | 0.73 | 0.80 | 37 | empty |
| 4 | 56 | 0.66 | 0.96 | 23 | empty |
| 5 | 453 | 0.64 | 0.78 | 35 | empty |
Interfaces
26 interfaces between chains.
- A–B · 2279 Ų buried · 36 hydrogen bonds · protein-protein
- F–G · 2042 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1176 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 1158 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1147 Ų buried · 110 hydrogen bonds · nucleic-nucleic
Compared structures
- 5N9G · TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1- · the same entry in another collection · chain J against J, TM-score 1.00
- P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9HAW0 · AlphaFold monomer V2.0 prediction for transcription factor iiib 50 kda subunit (Q9HAW0) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 Q9HAW0
- Every structure of UniProt P20226
- Every structure of UniProt A6H8Y1
- Elsewhere: RCSB PDB 5N9G · PDBe 5N9G · UniProt Q9HAW0 · UniProt P20226 · UniProt A6H8Y1
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