MolNFT v1 · #181075 · protein
Structure of the salmonella enterica CD-ntase cdnd in complex with GTP
7LJM: “Structure of the salmonella enterica CD-ntase cdnd in complex with GTP”. X-ray diffraction, 2 ligands (GTP, MG), 8 pockets (best druggability 0.72). MolNFT v1 #181075 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LJM
- Type
- protein
- Length
- 689 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD-ntase
- UniProt
- A0A728KSL7
- Ligands
- GTP, MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD-ntase | protein | 348 | 48% helix, 12% strand | A0A728KSL7 |
| B | CD-ntase | protein | 341 | 49% helix, 12% strand | A0A728KSL7 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.72 | 0.78 | 53 | MG, GTP |
| 2 | 800 | 0.72 | 0.77 | 52 | MG, GTP |
| 3 | 315 | 0.67 | 0.82 | 30 | empty |
| 4 | 65 | 0.46 | 0.83 | 16 | empty |
| 5 | 61 | 0.45 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 599 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7LJM · Structure of the Salmonella enterica CD-NTase CdnD in complex with GTP · 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 A0A728KSL7
- Elsewhere: RCSB PDB 7LJM · PDBe 7LJM · UniProt A0A728KSL7
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