MolNFT v1 · #181076 · protein
Structure of the bradyrhizobium diazoefficiens CD-ntase cdng in complex with GTP
7LJN: “Structure of the bradyrhizobium diazoefficiens CD-ntase cdng in complex with GTP”. X-ray diffraction, 2 ligands (GTP, MG), 16 pockets (best druggability 0.78). MolNFT v1 #181076 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7LJN
- Type
- protein
- Length
- 1,353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD-ntase
- UniProt
- Q89Y83
- Ligands
- GTP, MG
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD-ntase | protein | 342 | 48% helix, 15% strand | Q89Y83 |
| B | CD-ntase | protein | 335 | 48% helix, 16% strand | Q89Y83 |
| C | CD-ntase | protein | 337 | 47% helix, 16% strand | Q89Y83 |
| D | CD-ntase | protein | 339 | 48% helix, 16% strand | Q89Y83 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.78 | 0.82 | 49 | GTP, MG |
| 2 | 988 | 0.78 | 0.80 | 69 | GTP, MG |
| 3 | 926 | 0.77 | 0.80 | 66 | GTP, MG |
| 4 | 790 | 0.76 | 0.80 | 48 | GTP, MG |
| 5 | 248 | 0.70 | 0.86 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 713 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 268 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 252 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7LJN · Structure of the Bradyrhizobium diazoefficiens CD-NTase CdnG 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 Q89Y83
- Elsewhere: RCSB PDB 7LJN · PDBe 7LJN · UniProt Q89Y83
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