MolNFT v1 · #15841 · protein + DNA
Crystal structure of a yeast TFIIA/TBP/DNA complex
1NH2 · 5'-D(*TP*GP*TP*AP*(5IU)P*GP*TP*AP*TP*AP*(5IU)…: “Crystal structure of a yeast TFIIA/TBP/DNA complex”. X-ray diffraction, 5 pockets (best druggability 0.65). MolNFT v1 #15841 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1NH2
- Type
- protein + DNA
- Length
- 412 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*TP*AP*(5IU)P*GP*TP*AP*TP*AP*(5IU) P*AP*AP*AP*AP*C)-3'; 5'…
- UniProt
- P13393, P32773, P32774
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'-D(*TP*GP*TP*AP*(5IU)P*GP*TP*AP*TP*AP*(5IU) P*AP*AP*AP*AP*C)-3' | dna | 16 | — | — |
| F | 5'- D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3' | dna | 16 | — | — |
| A | Transcription initiation factor tfiid | protein | 180 | 27% helix, 37% strand | P13393 |
| B | Transcription initiation factor iia large chain | protein | 46 | 85% helix, 0% strand | P32773 |
| C | Transcription initiation factor iia large chain | protein | 50 | 0% helix, 78% strand | P32774 |
| D | Transcription initiation factor iia small chain | protein | 104 | 38% helix, 40% strand | P32773 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.65 | 0.76 | 39 | empty |
| 2 | 64 | 0.52 | 0.86 | 15 | empty |
| 3 | 106 | 0.45 | 0.79 | 21 | empty |
| 4 | 176 | 0.40 | 0.73 | 20 | empty |
| 5 | 52 | 0.33 | 0.78 | 16 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1723 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1098 Ų buried · 7 hydrogen bonds · protein-protein
- E–A · 796 Ų buried · 6 hydrogen bonds · protein-nucleic
- F–A · 789 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–F · 696 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1NH2 · Crystal structure of a yeast TFIIA/TBP/DNA complex · the same entry in another collection · chain D against D, TM-score 1.00
- P13393 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P13393) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P32773 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia large subunit… · a predicted model of the same protein · chain B against A, TM-score 0.96
- P32774 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 2… · a predicted model of the same protein · chain C against A, TM-score 0.77
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 P13393
- Every structure of UniProt P32773
- Every structure of UniProt P32774
- Elsewhere: RCSB PDB 1NH2 · PDBe 1NH2 · UniProt P13393 · UniProt P32773 · UniProt P32774
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