Research workbench
Structure of PKD1L3-CTD/PKD2L1 in apo state
Analyse Structure of PKD1L3-CTD/PKD2L1 in apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D7E
- Type
- protein
- Length
- 1,878 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycystic kidney disease 2-like 1 protein; Polycystic kidney disease protein 1-like 3
- UniProt
- A2A259, Q2EG98
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Polycystic kidney disease 2-like 1 protein | protein | 482 | 50% helix, 12% strand | A2A259 |
| C | Polycystic kidney disease 2-like 1 protein | protein | 474 | 46% helix, 12% strand | A2A259 |
| D | Polycystic kidney disease 2-like 1 protein | protein | 471 | 49% helix, 12% strand | A2A259 |
| A | Polycystic kidney disease protein 1-like 3 | protein | 451 | 45% helix, 11% strand | Q2EG98 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, C, D, A
- CA · Calcium ion · metal · 3 copies · chains 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.83 | 0.86 | 101 | empty |
| 2 | 970 | 0.79 | 0.81 | 103 | empty |
| 3 | 679 | 0.79 | 0.84 | 80 | empty |
| 4 | 523 | 0.79 | 0.85 | 60 | empty |
| 5 | 593 | 0.73 | 0.81 | 72 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3602 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3487 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 3000 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 2940 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 150 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 7D7E · Structure of PKD1L3-CTD/PKD2L1 in apo state · the same entry in another collection · chain A against A, TM-score 1.00
- A2A259 · AlphaFold monomer V2.0 prediction for polycystic kidney disease 2-like 1 protein (A2A259) · a predicted model of the same protein · chain D against A, TM-score 0.94
- Q2EG98 · AlphaFold monomer V2.0 prediction for polycystic kidney disease protein 1-like 3 (Q2EG98) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 A2A259
- Every structure of UniProt Q2EG98
- Elsewhere: RCSB PDB 7D7E · PDBe 7D7E · UniProt A2A259 · UniProt Q2EG98
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