MolNFT v1 · #57304 · protein
Crystal structure of lump complexed with 6,7-dimethyl-8-(1'- D-ribityl) lumazine
3A3G · Lumazine protein: “Crystal structure of lump complexed with 6,7-dimethyl-8-(1'- D-ribityl) lumazine”. X-ray diffraction, 1 ligand (DLZ), 5 pockets (best druggability 0.61). MolNFT v1 #57304 on GenesisL1: 3D structure, binding sites…
- PDB
- 3A3G
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lumazine protein
- UniProt
- C4TPG1
- Ligands
- DLZ
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lumazine protein | protein | 180 | 8% helix, 47% strand | C4TPG1 |
| B | Lumazine protein | protein | 177 | 11% helix, 47% strand | C4TPG1 |
Ligands and binding sites
- DLZ · 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.61 | 0.77 | 43 | DLZ |
| 2 | 82 | 0.41 | 0.79 | 15 | empty |
| 3 | 88 | 0.38 | 0.77 | 19 | empty |
| 4 | 51 | 0.32 | 0.77 | 16 | empty |
| 5 | 63 | 0.26 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 364 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3A3G · Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-ribityl) lumazine · 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 C4TPG1
- Elsewhere: RCSB PDB 3A3G · PDBe 3A3G · UniProt C4TPG1
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