MolNFT v1 · #103067 · protein
Vala (2-epi-5-epi-valiolone synthase) from streptomyces hygroscopicus subsp. jinggangensis 5008 with NAD+ and ZN2+ bound
4P53 · Cyclase: “Vala (2-epi-5-epi-valiolone synthase) from streptomyces hygroscopicus subsp. jinggangensis 5008 with NAD+ and…”. X-ray diffraction, 2 ligands (NAI, ZN), 2 pockets (best druggability 0.80). MolNFT v1 #103067 on GenesisL1…
- PDB
- 4P53
- Type
- protein
- Length
- 360 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclase
- UniProt
- H2K887
- Ligands
- NAI, ZN
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclase | protein | 360 | 53% helix, 15% strand | H2K887 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.80 | 0.84 | 72 | NAI |
| 2 | 52 | 0.25 | 0.73 | 15 | empty |
Compared structures
- 4P53 · ValA (2-epi-5-epi-valiolone synthase) from Streptomyces hygroscopicus subsp.… · the same entry in another collection · chain A against A, TM-score 1.00
- H2K887 · AlphaFold monomer V2.0 prediction for 2-epi-5-epi-valiolone synthase (H2K887) · a predicted model of the same protein · 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 H2K887
- Elsewhere: RCSB PDB 4P53 · PDBe 4P53 · UniProt H2K887
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