MolNFT v1 · #160861 · protein
Vibrio cholerae lapd S helix-ggdef-eal (bound to C-di-gmp)
6PWK · Ggdef and eal domain-containing protein: “Vibrio cholerae lapd S helix-ggdef-eal (bound to C-di-gmp)”. X-ray diffraction, 2 ligands (C2E, MG), 8 pockets (best druggability 0.79). MolNFT v1 #160861 on GenesisL1: 3D structure, binding…
- PDB
- 6PWK
- Type
- protein
- Length
- 811 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ggdef and eal domain-containing protein
- UniProt
- A0A0H6T0A6
- Ligands
- C2E, MG
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ggdef and eal domain-containing protein | protein | 406 | 50% helix, 20% strand | A0A0H6T0A6 |
| B | Ggdef and eal domain-containing protein | protein | 405 | 51% helix, 21% strand | A0A0H6T0A6 |
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 · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.79 | 0.81 | 85 | C2E |
| 2 | 977 | 0.78 | 0.80 | 75 | C2E |
| 3 | 195 | 0.49 | 0.76 | 24 | empty |
| 4 | 87 | 0.41 | 0.78 | 14 | empty |
| 5 | 55 | 0.39 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1080 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6PWK · Vibrio cholerae LapD S helix-GGDEF-EAL (bound to c-di-GMP) · 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 A0A0H6T0A6
- Elsewhere: RCSB PDB 6PWK · PDBe 6PWK · UniProt A0A0H6T0A6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.