MolNFT v1 · #141366 · protein
Crystal structure of a cyclase filc from fischerella sp. in complex with cyclo-L-arg-D-pro
5Z53 · 12-epi-hapalindole U synthase: “Crystal structure of a cyclase filc from fischerella sp. in complex with cyclo-L-arg-D-pro”. X-ray diffraction, 3 ligands (0HZ, CA, SO4), 14 pockets (best druggability 0.80). MolNFT v1 #141366 on…
- PDB
- 5Z53
- Type
- protein
- Length
- 797 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12-epi-hapalindole U synthase
- UniProt
- A0A1P8VSI6
- Ligands
- 0HZ, CA, SO4
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 12-epi-hapalindole U synthase | protein | 199 | 0% helix, 43% strand | A0A1P8VSI6 |
| D | 12-epi-hapalindole U synthase | protein | 200 | 0% helix, 44% strand | A0A1P8VSI6 |
Ligands and binding sites
- 0HZ · amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.80 | 0.97 | 25 | 0HZ |
| 2 | 137 | 0.80 | 0.97 | 25 | 0HZ |
| 3 | 229 | 0.80 | 0.93 | 37 | 0HZ |
| 4 | 345 | 0.80 | 0.89 | 43 | 0HZ |
| 5 | 122 | 0.66 | 0.89 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–D · 915 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 871 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 840 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5Z53 · Crystal structure of a cyclase Filc from Fischerella sp. in complex with cyclo-L-Arg-D-Pro · 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 A0A1P8VSI6
- Elsewhere: RCSB PDB 5Z53 · PDBe 5Z53 · UniProt A0A1P8VSI6
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