MolNFT v1 · #126100 · protein
Carboxysome shell protein ccmp from synechococcus elongatus pcc 7942
5LSR: “Carboxysome shell protein ccmp from synechococcus elongatus pcc 7942”. X-ray diffraction, 1 ligand (SCN), 2 pockets (best druggability 0.74). MolNFT v1 #126100 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LSR
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ccmp
- UniProt
- Q31QW7
- Ligands
- SCN
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ccmp | protein | 205 | 40% helix, 30% strand | Q31QW7 |
| B | Ccmp | protein | 206 | 39% helix, 30% strand | Q31QW7 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.74 | 0.79 | 69 | empty |
| 2 | 346 | 0.65 | 0.80 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1071 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1025 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1015 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5LSR · Carboxysome shell protein CcmP from Synechococcus elongatus PCC 7942 · the same entry in another collection · chain A against A, TM-score 1.00
- Q31QW7 · AlphaFold monomer V2.0 prediction for carboxysome shell protein ccmp (Q31QW7) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q31QW7
- Elsewhere: RCSB PDB 5LSR · PDBe 5LSR · UniProt Q31QW7
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