MolNFT v1 · #141367 · protein
Crystal structure of a cyclase HPIU5 from fischerella sp. atcc 43239 in complex with cyclo-L-arg-D-pro
5Z54 · 12-epi-hapalindole C/U synthase: “Crystal structure of a cyclase HPIU5 from fischerella sp. atcc 43239 in complex with cyclo-L-arg-D-pro”. X-ray diffraction, 2 ligands (0HZ, CA), 6 pockets (best druggability 0.87). MolNFT v1 #141367…
- PDB
- 5Z54
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12-epi-hapalindole C/U synthase
- UniProt
- A0A076NBW8
- Ligands
- 0HZ, CA
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 12-epi-hapalindole C/U synthase | protein | 199 | 0% helix, 45% strand | A0A076NBW8 |
| C, D | 12-epi-hapalindole C/U synthase | protein | 198 | 0% helix, 45% strand | A0A076NBW8 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.87 | 0.96 | 45 | 0HZ |
| 2 | 161 | 0.81 | 0.96 | 24 | 0HZ |
| 3 | 153 | 0.80 | 0.96 | 21 | 0HZ |
| 4 | 314 | 0.53 | 0.74 | 39 | empty |
| 5 | 267 | 0.50 | 0.74 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 943 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 172 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 138 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Z54 · Crystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239 in complex with… · 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 A0A076NBW8
- Elsewhere: RCSB PDB 5Z54 · PDBe 5Z54 · UniProt A0A076NBW8
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