MolNFT v1 · #88548 · protein
Glxr bound to camp
4CYD · Probable transcription regulator: “Glxr bound to camp”. X-ray diffraction, 1 ligand (CMP), 12 pockets (best druggability 0.84). MolNFT v1 #88548 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CYD
- Type
- protein
- Length
- 928 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transcription regulator; Probable expression tag
- UniProt
- H7C677
- Ligands
- CMP
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable transcription regulator | protein | 223 | 45% helix, 24% strand | H7C677 |
| B, C | Probable transcription regulator | protein | 225 | 47% helix, 25% strand | H7C677 |
| D | Probable transcription regulator | protein | 214 | 44% helix, 22% strand | H7C677 |
| F | Probable expression tag | protein | 21 | 33% helix, 0% strand | — |
| H | Probable expression tag | protein | 20 | 35% helix, 0% strand | — |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 4 copies · chains A, C, B, D, F, H
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.84 | 0.94 | 45 | CMP |
| 2 | 858 | 0.81 | 0.84 | 92 | CMP |
| 3 | 532 | 0.80 | 0.86 | 60 | CMP, GOL |
| 4 | 471 | 0.79 | 0.87 | 53 | CMP |
| 5 | 1039 | 0.76 | 0.79 | 84 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1886 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1836 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 845 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 818 Ų buried · 15 hydrogen bonds · protein-protein
- D–H · 447 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4CYD · GlxR bound to cAMP · 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 H7C677
- Elsewhere: RCSB PDB 4CYD · PDBe 4CYD · UniProt H7C677
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