MolNFT v1 · #153812 · protein
Crystal structure of mada
6JQH: “Crystal structure of mada”. X-ray diffraction, 1 ligand (FAD), 11 pockets (best druggability 0.82). MolNFT v1 #153812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JQH
- Type
- protein
- Length
- 1,017 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mada
- Ligands
- FAD
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mada | protein | 504 | 36% helix, 21% strand | — |
| B | Mada | protein | 513 | 36% helix, 21% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.82 | 0.82 | 79 | FAD |
| 2 | 1005 | 0.81 | 0.82 | 84 | FAD |
| 3 | 64 | 0.71 | 0.96 | 16 | empty |
| 4 | 106 | 0.41 | 0.77 | 23 | empty |
| 5 | 98 | 0.39 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 792 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (flavinylation, disulfide).
Compared structures
- 6JQH · Crystal structure of MaDA · 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
- Elsewhere: RCSB PDB 6JQH · PDBe 6JQH
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