MolNFT v1 · #124486 · protein
Structure of K. pneumonia mrkh-C-di-gmp complex
5KGO · Flagellar brake protein ycgr: “Structure of K. pneumonia mrkh-C-di-gmp complex”. X-ray diffraction, 1 ligand (C2E), 4 pockets (best druggability 0.65). MolNFT v1 #124486 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KGO
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flagellar brake protein ycgr
- UniProt
- G3FT00
- Ligands
- C2E
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Flagellar brake protein ycgr | protein | 227 | 16% helix, 47% strand | G3FT00 |
| A | Flagellar brake protein ycgr | protein | 219 | 17% helix, 48% strand | G3FT00 |
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 D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.65 | 0.80 | 46 | empty |
| 2 | 485 | 0.64 | 0.77 | 35 | C2E |
| 3 | 312 | 0.50 | 0.73 | 38 | C2E |
| 4 | 57 | 0.28 | 0.75 | 17 | C2E |
Interfaces
1 interface between chains.
- D–A · 640 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5KGO · Structure of K. pneumonia MrkH-c-di-GMP complex · the same entry in another collection · chain D against D, 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 G3FT00
- Elsewhere: RCSB PDB 5KGO · PDBe 5KGO · UniProt G3FT00
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