MolNFT v1 · #123435 · protein
Crystal structure of IDNL1
5JJQ · AMP-dependent synthetase and ligase: “Crystal structure of IDNL1”. X-ray diffraction, 2 ligands (6L1, CL), 20 pockets (best druggability 0.81). MolNFT v1 #123435 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JJQ
- Type
- protein
- Length
- 1,951 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMP-dependent synthetase and ligase
- UniProt
- A0A077KT11
- Ligands
- 6L1, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMP-dependent synthetase and ligase | protein | 488 | 30% helix, 28% strand | A0A077KT11 |
| B | AMP-dependent synthetase and ligase | protein | 487 | 31% helix, 27% strand | A0A077KT11 |
| C | AMP-dependent synthetase and ligase | protein | 489 | 30% helix, 28% strand | A0A077KT11 |
| D | AMP-dependent synthetase and ligase | protein | 487 | 32% helix, 27% strand | A0A077KT11 |
Ligands and binding sites
- 6L1 · 5'-O-[(R)-{[(3S)-3-aminobutanoyl]oxy}(hydroxy)phosphoryl]adenosine · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.81 | 0.82 | 96 | 6L1 |
| 2 | 1015 | 0.81 | 0.82 | 90 | 6L1 |
| 3 | 1044 | 0.79 | 0.80 | 102 | 6L1 |
| 4 | 1159 | 0.78 | 0.80 | 102 | 6L1 |
| 5 | 81 | 0.75 | 0.98 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2349 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2221 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 674 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 220 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JJQ · Crystal structure of IdnL1 · 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 A0A077KT11
- Elsewhere: RCSB PDB 5JJQ · PDBe 5JJQ · UniProt A0A077KT11
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