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DNA complexed structure of the key transcription factor initiating development in sporulation bacteria
Analyse DNA complexed structure of the key transcription factor initiating development… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LQ1
- Type
- protein + DNA
- Length
- 493 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'; 5'…
- UniProt
- P06534
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | 5'- D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3' | dna | 16 | — | — |
| F, H | 5'- D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3' | dna | 16 | — | — |
| A | Stage 0 sporulation protein a | protein | 107 | 75% helix, 0% strand | P06534 |
| B | Stage 0 sporulation protein a | protein | 103 | 71% helix, 0% strand | P06534 |
| C | Stage 0 sporulation protein a | protein | 112 | 67% helix, 0% strand | P06534 |
| D | Stage 0 sporulation protein a | protein | 107 | 74% helix, 0% strand | P06534 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.69 | 0.79 | 63 | empty |
| 2 | 532 | 0.67 | 0.78 | 63 | empty |
| 3 | 363 | 0.56 | 0.75 | 35 | empty |
| 4 | 65 | 0.41 | 0.81 | 15 | empty |
| 5 | 128 | 0.40 | 0.75 | 17 | empty |
Interfaces
18 interfaces between chains.
- G–H · 716 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- E–F · 704 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- E–D · 479 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 467 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 458 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1LQ1 · DNA Complexed Structure of the Key Transcription Factor Initiating Development in… · the same entry in another collection · chain C against C, TM-score 1.00
- P06534 · AlphaFold monomer V2.0 prediction for stage 0 sporulation protein a (P06534) · a predicted model of the same protein · chain B 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 P06534
- Elsewhere: RCSB PDB 1LQ1 · PDBe 1LQ1 · UniProt P06534
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