MolNFT v1 · #3811 · protein + DNA
Tata-binding PROTEIN/TRANSCRIPTION factor (II)B/BRE+TATA-box complex from pyrococcus woesei
1D3U · DNA 24-mer: BRE+TATA-box: “Tata-binding PROTEIN/TRANSCRIPTION factor (II)B/BRE+TATA-box complex from pyrococcus woesei”. X-ray diffraction, 8 pockets (best druggability 0.74). MolNFT v1 #3811 on GenesisL1: 3D structure, binding…
- PDB
- 1D3U
- Type
- protein + DNA
- Length
- 429 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA 24-mer: BRE+TATA-box; DNA 23-mer: BRE+TATA-box; Tata-binding protein; Transcription…
- UniProt
- P62001, P61999
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA 24-mer: BRE+TATA-box | dna | 24 | — | — |
| D | DNA 23-mer: BRE+TATA-box | dna | 23 | — | — |
| A | Tata-binding protein | protein | 181 | 23% helix, 36% strand | P62001 |
| B | Transcription initiation factor iib | protein | 201 | 71% helix, 0% strand | P61999 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.74 | 0.89 | 43 | empty |
| 2 | 577 | 0.65 | 0.77 | 28 | empty |
| 3 | 261 | 0.60 | 0.80 | 37 | empty |
| 4 | 96 | 0.53 | 0.84 | 27 | empty |
| 5 | 95 | 0.44 | 0.79 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 987 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- D–A · 817 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 804 Ų buried · 13 hydrogen bonds · protein-protein
- C–A · 804 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–B · 594 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1D3U · Tata-binding PROTEIN/TRANSCRIPTION factor (II)B/BRE+TATA-box complex from pyrococcus… · the same entry in another collection · chain C against C, TM-score 1.00
- P62001 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P62001) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P61999 · AlphaFold monomer V2.0 prediction for transcription initiation factor iib (P61999) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P62001
- Every structure of UniProt P61999
- Elsewhere: RCSB PDB 1D3U · PDBe 1D3U · UniProt P62001 · UniProt P61999
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