MolNFT v1 · #127026 · protein
PA3825-eal ca-cdg structure
5MKG · Diguanylate phosphodiesterase: “PA3825-eal ca-cdg structure”. X-ray diffraction, 2 ligands (C2E, CA), 6 pockets (best druggability 0.72). MolNFT v1 #127026 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MKG
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate phosphodiesterase
- UniProt
- A0A140SMD7
- Ligands
- C2E, CA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate phosphodiesterase | protein | 248 | 42% helix, 23% strand | A0A140SMD7 |
| B | Diguanylate phosphodiesterase | protein | 249 | 45% helix, 22% strand | A0A140SMD7 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.72 | 0.80 | 71 | CA, C2E |
| 2 | 435 | 0.66 | 0.79 | 42 | CA, C2E |
| 3 | 65 | 0.63 | 0.92 | 21 | empty |
| 4 | 58 | 0.62 | 0.92 | 19 | empty |
| 5 | 310 | 0.56 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 493 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5MKG · PA3825-EAL Ca-CdG Structure · the same entry in another collection · chain B against B, 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 A0A140SMD7
- Elsewhere: RCSB PDB 5MKG · PDBe 5MKG · UniProt A0A140SMD7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.