MolNFT v1 · #181716 · protein
Crystal structure of galactonate dehydratase from brucella melitensis biovar abortus 2308
7M3K: “Crystal structure of galactonate dehydratase from brucella melitensis biovar abortus 2308”. X-ray diffraction, 2 ligands (ZN, CL), 5 pockets (best druggability 0.66). MolNFT v1 #181716 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7M3K
- Type
- protein
- Length
- 587 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactonate dehydratase
- EC
- 4.2.1.6
- UniProt
- Q2YJ21
- Ligands
- ZN, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactonate dehydratase (EC 4.2.1.6) | protein | 587 | 39% helix, 16% strand | Q2YJ21 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.66 | 0.77 | 65 | ZN |
| 2 | 132 | 0.54 | 0.82 | 26 | empty |
| 3 | 51 | 0.43 | 0.84 | 15 | empty |
| 4 | 58 | 0.32 | 0.75 | 15 | empty |
| 5 | 67 | 0.28 | 0.73 | 24 | PEG |
Compared structures
- 7M3K · Crystal Structure of Galactonate dehydratase from Brucella melitensis biovar Abortus 2308 · 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 Q2YJ21
- Elsewhere: RCSB PDB 7M3K · PDBe 7M3K · UniProt Q2YJ21
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