MolNFT v1 · #141079 · protein
Crystal structure of a cyclase HPIU5 from fischerella sp. atcc 43239
5YVL: “Crystal structure of a cyclase HPIU5 from fischerella sp. atcc 43239”. X-ray diffraction, 1 ligand (CA), 14 pockets (best druggability 0.75). MolNFT v1 #141079 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YVL
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclase
- UniProt
- A0A076NBW8
- Ligands
- CA
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclase | protein | 200 | 0% helix, 44% strand | A0A076NBW8 |
| B | Cyclase | protein | 198 | 0% helix, 44% strand | A0A076NBW8 |
| C | Cyclase | protein | 199 | 0% helix, 44% strand | A0A076NBW8 |
| D | Cyclase | protein | 206 | 0% helix, 42% strand | A0A076NBW8 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 3 copies · chains B, C, 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 | 132 | 0.75 | 0.93 | 25 | empty |
| 2 | 118 | 0.68 | 0.90 | 27 | empty |
| 3 | 132 | 0.68 | 0.89 | 28 | empty |
| 4 | 121 | 0.67 | 0.89 | 27 | empty |
| 5 | 124 | 0.66 | 0.89 | 29 | empty |
Interfaces
4 interfaces between chains.
- A–B · 978 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 901 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 119 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 106 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5YVL · Crystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239 · the same entry in another collection · chain B against B, 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 5YVL · PDBe 5YVL · UniProt A0A076NBW8
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