MolNFT v1 · #41035 · protein
PAE2307 with AMP
2JB7 · Hypothetical protein PAE2307: “PAE2307 with AMP”. X-ray diffraction, 1 ligand (AMP), 4 pockets (best druggability 0.79). MolNFT v1 #41035 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2JB7
- Type
- protein
- Length
- 488 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PAE2307
- UniProt
- Q8ZVF7
- Ligands
- AMP
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein PAE2307 | protein | 163 | 29% helix, 36% strand | Q8ZVF7 |
| C | Hypothetical protein PAE2307 | protein | 162 | 29% helix, 36% strand | Q8ZVF7 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, C, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.79 | 0.95 | 22 | ACT |
| 2 | 206 | 0.53 | 0.77 | 26 | AMP |
| 3 | 147 | 0.49 | 0.78 | 24 | AMP |
| 4 | 159 | 0.49 | 0.77 | 24 | AMP |
Interfaces
3 interfaces between chains.
- A–B · 1949 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 1942 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1937 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 2JB7 · PAE2307 with AMP · 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 Q8ZVF7
- Elsewhere: RCSB PDB 2JB7 · PDBe 2JB7 · UniProt Q8ZVF7
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