MolNFT v1 · #128417 · protein
Crystal structure of hexameric cbs-CP12 protein from bloom-forming cyanobacteria, yb-derivative at 2.8 a resolution
5NPL · Similar to TR|Q8YYT1|Q8YYT1: “Crystal structure of hexameric cbs-CP12 protein from bloom-forming cyanobacteria, yb-derivative at 2.8 a…”. X-ray diffraction, 2 ligands (DO3, YB), 10 pockets (best druggability 0.79). MolNFT v1 #128417…
- PDB
- 5NPL
- Type
- protein
- Length
- 537 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to TR|Q8YYT1|Q8YYT1
- UniProt
- A8YJ50
- Ligands
- DO3, YB
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Similar to TR|Q8YYT1|Q8YYT1 | protein | 181 | 46% helix, 17% strand | A8YJ50 |
| B | Similar to TR|Q8YYT1|Q8YYT1 | protein | 177 | 46% helix, 17% strand | A8YJ50 |
| C | Similar to TR|Q8YYT1|Q8YYT1 | protein | 179 | 45% helix, 17% strand | A8YJ50 |
Ligands and binding sites
- DO3 · 10-((2R)-2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane 1,4,7-triacetic acid · ligand · 2 copies · chains A, B
- YB · Ytterbium (III) ion · metal · 17 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.79 | 0.88 | 41 | empty |
| 2 | 266 | 0.58 | 0.78 | 25 | empty |
| 3 | 63 | 0.54 | 0.88 | 23 | empty |
| 4 | 188 | 0.53 | 0.78 | 30 | empty |
| 5 | 195 | 0.50 | 0.76 | 23 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1877 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1566 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5NPL · Crystal structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria… · 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 A8YJ50
- Elsewhere: RCSB PDB 5NPL · PDBe 5NPL · UniProt A8YJ50
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