MolNFT v1 · #128319 · protein
Structure of hexameric cbs-CP12 protein from bloom-forming cyanobacteria
5NMU: “Structure of hexameric cbs-CP12 protein from bloom-forming cyanobacteria”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.79). MolNFT v1 #128319 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NMU
- Type
- protein
- Length
- 521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cbs-CP12
- UniProt
- A8YJ50
- Ligands
- CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cbs-CP12 | protein | 177 | 47% helix, 17% strand | A8YJ50 |
| B | Cbs-CP12 | protein | 173 | 45% helix, 17% strand | A8YJ50 |
| C | Cbs-CP12 | protein | 171 | 42% helix, 18% strand | A8YJ50 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.79 | 0.88 | 41 | empty |
| 2 | 297 | 0.59 | 0.78 | 37 | empty |
| 3 | 59 | 0.58 | 0.90 | 19 | empty |
| 4 | 179 | 0.52 | 0.78 | 28 | empty |
| 5 | 87 | 0.48 | 0.82 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1881 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1564 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5NMU · 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 5NMU · PDBe 5NMU · UniProt A8YJ50
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