MolNFT v1 · #64865 · protein
Klebsiella pneumoniae BLRP1 with FMN and cyclic digmp, no metal ions
3GFY: “Klebsiella pneumoniae BLRP1 with FMN and cyclic digmp, no metal ions”. X-ray diffraction, 2 ligands (C2E, FMN), 16 pockets (best druggability 0.69). MolNFT v1 #64865 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GFY
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Klebsiella pneumoniae BLRP1
- UniProt
- A6T8V8
- Ligands
- C2E, FMN
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Klebsiella pneumoniae BLRP1 | protein | 372 | 39% helix, 24% strand | A6T8V8 |
| B | Klebsiella pneumoniae BLRP1 | protein | 374 | 42% helix, 24% strand | A6T8V8 |
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
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.69 | 0.97 | 19 | empty |
| 2 | 59 | 0.66 | 0.95 | 18 | empty |
| 3 | 171 | 0.65 | 0.85 | 20 | FMN |
| 4 | 153 | 0.64 | 0.86 | 20 | FMN |
| 5 | 299 | 0.63 | 0.80 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2240 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3GFY · Klebsiella pneumoniae BlrP1 with FMN and cyclic diGMP, no metal ions · 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 A6T8V8
- Elsewhere: RCSB PDB 3GFY · PDBe 3GFY · UniProt A6T8V8
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