MolNFT v1 · #176585 · protein
Structure of ATP-grasp ligase psnb complexed with precursor peptide PSNA2 and amppnp
7DRN · ATP-grasp domain-containing protein: “Structure of ATP-grasp ligase psnb complexed with precursor peptide PSNA2 and amppnp”. X-ray diffraction, 1 ligand (ANP), 12 pockets (best druggability 0.78). MolNFT v1 #176585 on GenesisL1: 3D…
- PDB
- 7DRN
- Type
- protein
- Length
- 1,248 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-grasp domain-containing protein; PSNA214-38, precursor peptide
- UniProt
- A6G4D7, A6GH40
- Ligands
- ANP
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-grasp domain-containing protein | protein | 311 | 39% helix, 23% strand | A6G4D7 |
| B | ATP-grasp domain-containing protein | protein | 295 | 37% helix, 23% strand | A6G4D7 |
| C | ATP-grasp domain-containing protein | protein | 311 | 40% helix, 25% strand | A6G4D7 |
| D | ATP-grasp domain-containing protein | protein | 297 | 40% helix, 24% strand | A6G4D7 |
| E, F | PSNA214-38, precursor peptide | protein | 17 | 18% helix, 0% strand | A6GH40 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.78 | 0.80 | 116 | empty |
| 2 | 1047 | 0.78 | 0.80 | 81 | ANP |
| 3 | 1019 | 0.74 | 0.77 | 89 | empty |
| 4 | 385 | 0.60 | 0.76 | 34 | ANP |
| 5 | 160 | 0.51 | 0.79 | 28 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2420 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2394 Ų buried · 45 hydrogen bonds · protein-protein
- C–F · 843 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 806 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 623 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7DRN · Structure of ATP-grasp ligase PsnB complexed with precursor peptide PsnA2 and AMPPNP · 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 A6G4D7
- Every structure of UniProt A6GH40
- Elsewhere: RCSB PDB 7DRN · PDBe 7DRN · UniProt A6G4D7 · UniProt A6GH40
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