Research workbench
Crystal structure of a yeast BRF1-tbp-DNA ternary complex
Analyse Crystal structure of a yeast BRF1-tbp-DNA ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NGM
- Type
- protein + DNA
- Length
- 1,122 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T) -3'; 5'…
- UniProt
- P13393, P29056
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G, K, O | 5'- D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T) -3' | dna | 19 | — | — |
| D, H, L, P | 5'- D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G) -3' | dna | 19 | — | — |
| A, E, I, M | Transcription initiation factor tfiid | protein | 180 | 22% helix, 22% strand | P13393 |
| B, F | Transcription factor iiib BRF1 subunit | protein | 72 | 44% helix, 0% strand | P29056 |
| J, N | Transcription factor iiib BRF1 subunit | protein | 53 | 57% helix, 0% strand | P29056 |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.71 | 0.80 | 65 | empty |
| 2 | 165 | 0.50 | 0.78 | 25 | empty |
| 3 | 180 | 0.49 | 0.77 | 30 | empty |
| 4 | 183 | 0.48 | 0.76 | 28 | empty |
| 5 | 93 | 0.37 | 0.75 | 18 | empty |
Interfaces
31 interfaces between chains.
- A–B · 1996 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1940 Ų buried · 35 hydrogen bonds · protein-protein
- M–N · 1517 Ų buried · 28 hydrogen bonds · protein-protein
- I–J · 1488 Ų buried · 29 hydrogen bonds · protein-protein
- D–A · 870 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1NGM · Crystal structure of a yeast Brf1-TBP-DNA ternary complex · the same entry in another collection · chain N against N, 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 P13393
- Every structure of UniProt P29056
- Elsewhere: RCSB PDB 1NGM · PDBe 1NGM · UniProt P13393 · UniProt P29056
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.