MolNFT v1 · #110240 · protein + DNA
Crystal structure of agra lyttr domain in complex with promoters
4XQJ · Accessory gene regulator a: “Crystal structure of agra lyttr domain in complex with promoters”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.79). MolNFT v1 #110240 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4XQJ
- Type
- protein + DNA
- Length
- 246 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Accessory gene regulator a; DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3'); DNA…
- UniProt
- Q5HEG2
- Ligands
- CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Accessory gene regulator a | protein | 99 | 16% helix, 45% strand | Q5HEG2 |
| B | DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3') | dna | 12 | — | — |
| C, F | DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3') | dna | 13 | — | — |
| D | Accessory gene regulator a | protein | 98 | 11% helix, 49% strand | Q5HEG2 |
| E | DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains F
- EOH · Ethanol · additive · 14 copies · chains A, D, C, B, E, F
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.79 | 0.81 | 89 | EOH, EDO |
| 2 | 132 | 0.40 | 0.74 | 21 | empty |
| 3 | 116 | 0.36 | 0.74 | 16 | EOH, EDO |
| 4 | 85 | 0.34 | 0.76 | 12 | EOH, CA |
| 5 | 65 | 0.31 | 0.75 | 14 | EOH |
Interfaces
11 interfaces between chains.
- A–D · 680 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 548 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–F · 543 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 531 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- E–F · 502 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XQJ · Crystal structure of AgrA LytTR domain in complex with promoters · the same entry in another collection · chain F against F, TM-score 1.00
- Q5HEG2 · AlphaFold monomer V2.0 prediction for accessory gene regulator a (Q5HEG2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 4XQJ · PDBe 4XQJ · UniProt Q5HEG2
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