MolNFT v1 · #117603 · protein + DNA
Structure of a phop-DNA complex
5ED4 · Response regulator: “Structure of a phop-DNA complex”. X-ray diffraction, 1 ligand (CA), 15 pockets (best druggability 0.82). MolNFT v1 #117603 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ED4
- Type
- protein + DNA
- Length
- 981 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator; DNA (26-mer)
- EC
- 3.1.3.1
- UniProt
- A0A045J469
- Ligands
- CA
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Response regulator (EC 3.1.3.1) | protein | 222 | 40% helix, 21% strand | A0A045J469 |
| B | Response regulator (EC 3.1.3.1) | protein | 217 | 39% helix, 22% strand | A0A045J469 |
| C, G | DNA (26-mer) | dna | 26 | — | — |
| D, H | DNA (26-mer) | dna | 26 | — | — |
| E | Response regulator (EC 3.1.3.1) | protein | 224 | 38% helix, 21% strand | A0A045J469 |
| F | Response regulator (EC 3.1.3.1) | protein | 214 | 39% helix, 22% strand | A0A045J469 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, E, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D, E
- CAC · Cacodylate ion · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.82 | 0.83 | 94 | EDO |
| 2 | 919 | 0.80 | 0.83 | 79 | empty |
| 3 | 233 | 0.68 | 0.85 | 30 | empty |
| 4 | 136 | 0.53 | 0.81 | 24 | empty |
| 5 | 94 | 0.50 | 0.82 | 17 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1117 Ų buried · 116 hydrogen bonds · nucleic-nucleic
- G–H · 1111 Ų buried · 112 hydrogen bonds · nucleic-nucleic
- E–F · 856 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 804 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 486 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 5ED4 · Structure of a PhoP-DNA complex · the same entry in another collection · chain A against A, 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 A0A045J469
- Elsewhere: RCSB PDB 5ED4 · PDBe 5ED4 · UniProt A0A045J469
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.