Research workbench
Crystal structure of agra lyttr domain in complex with promoters
Analyse Crystal structure of agra lyttr domain in complex with promoters in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XQQ
- Type
- protein + DNA
- Length
- 460 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Accessory gene regulator a; DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)…
- UniProt
- Q5HEG2
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Accessory gene regulator a | protein | 99 | 16% helix, 51% strand | Q5HEG2 |
| B | Accessory gene regulator a | protein | 98 | 16% helix, 51% strand | Q5HEG2 |
| D | Accessory gene regulator a | protein | 100 | 16% helix, 50% strand | Q5HEG2 |
| E, G | DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)- 3') | dna | 16 | — | — |
| F, H | DNA (5'-D(*AP*TP*TP*TP*CP*TP*TP*AP*AP*CP*TP*AP*GP*TP*CP*G)- 3') | dna | 16 | — | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.51 | 0.76 | 18 | empty |
| 2 | 155 | 0.44 | 0.75 | 28 | empty |
| 3 | 174 | 0.43 | 0.75 | 23 | empty |
| 4 | 83 | 0.37 | 0.76 | 16 | empty |
| 5 | 78 | 0.30 | 0.73 | 16 | empty |
Interfaces
9 interfaces between chains.
- G–H · 665 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- E–F · 656 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- B–F · 440 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–E · 371 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 338 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4XQQ · Crystal structure of AgrA LytTR domain in complex with promoters · the same entry in another collection · chain H against H, TM-score 1.00
- Q5HEG2 · AlphaFold monomer V2.0 prediction for accessory gene regulator a (Q5HEG2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5HEG2
- Elsewhere: RCSB PDB 4XQQ · PDBe 4XQQ · UniProt Q5HEG2
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