MolNFT v1 · #28417 · protein
Crystal structure of the hmg-CoA lyase from brucella melitensis, northeast structural genomics target LR35.
1YDN · Hydroxymethylglutaryl-CoA lyase: “Crystal structure of the hmg-CoA lyase from brucella melitensis, northeast structural genomics target LR35.”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.89). MolNFT v1 #28417…
- PDB
- 1YDN
- Type
- protein
- Length
- 1,132 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxymethylglutaryl-CoA lyase
- EC
- 4.1.3.4
- UniProt
- Q8YEF2
- Ligands
- CA
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) | protein | 283 | 45% helix, 20% strand | Q8YEF2 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.89 | 0.91 | 102 | empty |
| 2 | 295 | 0.83 | 0.94 | 35 | CA |
| 3 | 712 | 0.80 | 0.84 | 72 | empty |
| 4 | 103 | 0.63 | 0.89 | 23 | empty |
| 5 | 53 | 0.49 | 0.87 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–C · 861 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 717 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 234 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 64 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1YDN · Crystal Structure of the HMG-CoA Lyase from Brucella melitensis, Northeast Structural… · 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 Q8YEF2
- Elsewhere: RCSB PDB 1YDN · PDBe 1YDN · UniProt Q8YEF2
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