MolNFT v1 · #124779 · protein
Crystal structure of the curacin biosynthetic pathway hmg synthase in complex with acetyl donor-acp
5KP8 · Curd: “Crystal structure of the curacin biosynthetic pathway hmg synthase in complex with acetyl donor-acp”. X-ray diffraction, 2 ligands (PNS, 6VG), 4 pockets (best druggability 0.76). MolNFT v1 #124779 on GenesisL1: 3D structure…
- PDB
- 5KP8
- Type
- protein
- Length
- 488 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Curd; Curb
- EC
- 2.3.3.10
- UniProt
- F4Y432, Q6DNF1
- Ligands
- PNS, 6VG
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Curd (EC 2.3.3.10) | protein | 410 | 41% helix, 25% strand | F4Y432 |
| B | Curb | protein | 78 | 58% helix, 0% strand | Q6DNF1 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · chains A, B
- 6VG · ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.76 | 0.83 | 82 | PNS, 6VG |
| 2 | 110 | 0.58 | 0.85 | 20 | empty |
| 3 | 112 | 0.43 | 0.77 | 19 | empty |
| 4 | 76 | 0.40 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 799 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 covalent (phosphopantetheinylation, covalent ligand).
Compared structures
- 5KP8 · Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Acetyl… · 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 F4Y432
- Every structure of UniProt Q6DNF1
- Elsewhere: RCSB PDB 5KP8 · PDBe 5KP8 · UniProt F4Y432 · UniProt Q6DNF1
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