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
- 4XQN
- Type
- protein + DNA
- Length
- 488 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3'); DNA…
- UniProt
- Q5HEG2
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E, H | DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3') | dna | 12 | — | — |
| C, F | DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3') | dna | 13 | — | — |
| I, L | DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3') | dna | 12 | — | — |
| K | DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3') | dna | 11 | — | — |
| A | Accessory gene regulator a | protein | 97 | 11% helix, 48% strand | Q5HEG2 |
| D, G, J | Accessory gene regulator a | protein | 98 | 14% helix, 51% strand | Q5HEG2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains C, J, I, H, K, L, D, E, F, G, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.74 | 0.78 | 63 | EDO |
| 2 | 886 | 0.73 | 0.78 | 50 | empty |
| 3 | 452 | 0.65 | 0.78 | 39 | EDO |
| 4 | 206 | 0.41 | 0.72 | 16 | empty |
| 5 | 128 | 0.40 | 0.75 | 22 | empty |
Interfaces
24 interfaces between chains.
- F–D · 547 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 538 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- E–F · 536 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- C–A · 535 Ų buried · 11 hydrogen bonds · protein-nucleic
- H–I · 519 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XQN · Crystal structure of AgrA LytTR domain in complex with promoters · the same entry in another collection · chain J against J, 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 Q5HEG2
- Elsewhere: RCSB PDB 4XQN · PDBe 4XQN · UniProt Q5HEG2
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