Research workbench
Cyanophycin synthetase 1 from synechocystis sp. UTEX2470 with ATP and 8X(ASP-arg)-asn
Analyse Cyanophycin synthetase 1 from synechocystis sp. UTEX2470 with ATP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LGQ
- Type
- protein
- Length
- 3,504 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyanophycin synthase; 8X(ASP-arg)-asn
- EC
- 6.3.2.29, 6.3.2.30
- UniProt
- A0A068N621
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cyanophycin synthase (EC 6.3.2.29, 6.3.2.30) | protein | 868 | 32% helix, 21% strand | A0A068N621 |
| E, F, G, H | 8X(ASP-arg)-asn | protein | 4 | 0% helix, 0% strand | — |
| I, J, K, L | 8X(ASP-arg)-asn | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, J, B, I, C, K, D, L
- MG · Magnesium ion · metal · 8 copies · chains A, J, B, I, C, K, D, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.78 | 0.80 | 88 | ATP |
| 2 | 918 | 0.78 | 0.80 | 80 | ATP |
| 3 | 977 | 0.78 | 0.80 | 88 | ATP |
| 4 | 923 | 0.77 | 0.80 | 82 | ATP |
| 5 | 780 | 0.77 | 0.81 | 78 | ATP, MG |
Interfaces
16 interfaces between chains.
- A–B · 1858 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1852 Ų buried · 16 hydrogen bonds · protein-protein
- D–H · 530 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 530 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 527 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (nonstandard).
Compared structures
- 7LGQ · Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 8x(Asp-Arg)-Asn · 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 A0A068N621
- Elsewhere: RCSB PDB 7LGQ · PDBe 7LGQ · UniProt A0A068N621
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