MolNFT v1 · #16332 · protein + DNA
Human TFIIA/TBP/DNA complex
1NVP · 5'- D(*GP*GP*GP*GP*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*G)-3': “Human TFIIA/TBP/DNA complex”. X-ray diffraction, 3 pockets (best druggability 0.64). MolNFT v1 #16332 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NVP
- Type
- protein + DNA
- Length
- 401 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*GP*GP*GP*GP*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*G)-3'; 5'…
- UniProt
- P20226, P52655, P52657
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'- D(*GP*GP*GP*GP*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*G)-3' | dna | 17 | — | — |
| F | 5'- D(*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*CP*CP*CP*C)-3' | dna | 17 | — | — |
| A | Tata box binding protein | protein | 180 | 26% helix, 38% strand | P20226 |
| B | Transcription initiation factor iia alpha chain | protein | 43 | 88% helix, 0% strand | P52655 |
| C | Transcription initiation factor iia beta chain | protein | 47 | 0% helix, 81% strand | P52655 |
| D | Transcription initiation factor iia gamma chain | protein | 97 | 41% helix, 39% strand | P52657 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.64 | 0.75 | 37 | empty |
| 2 | 70 | 0.45 | 0.82 | 20 | empty |
| 3 | 204 | 0.43 | 0.73 | 20 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1679 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 956 Ų buried · 6 hydrogen bonds · protein-protein
- E–A · 833 Ų buried · 7 hydrogen bonds · protein-nucleic
- F–A · 824 Ų buried · 10 hydrogen bonds · protein-nucleic
- E–F · 760 Ų buried · 77 hydrogen bonds · nucleic-nucleic
Compared structures
- 1NVP · Human TFIIA/TBP/DNA complex · the same entry in another collection · chain D against D, TM-score 1.00
- P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P52655 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 1… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P52657 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 2… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P20226
- Every structure of UniProt P52655
- Every structure of UniProt P52657
- Elsewhere: RCSB PDB 1NVP · PDBe 1NVP · UniProt P20226 · UniProt P52655 · UniProt P52657
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