MolNFT v1 · #175968 · protein
Structure of PKD1L3-CTD/PKD2L1 in calcium-bound state
7D7F · Polycystic kidney disease 2-like 1 protein: “Structure of PKD1L3-CTD/PKD2L1 in calcium-bound state”. Electron microscopy, 2 ligands (NAG, CA), 20 pockets (best druggability 0.82). MolNFT v1 #175968 on GenesisL1: 3D structure…
- PDB
- 7D7F
- Type
- protein
- Length
- 1,873 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 0.82
Structure
electron microscopy · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Polycystic kidney disease 2-like 1 protein | protein | 482 | 49% helix, 13% strand | A2A259 |
| C | Polycystic kidney disease 2-like 1 protein | protein | 474 | 51% helix, 13% strand | A2A259 |
| D | Polycystic kidney disease 2-like 1 protein | protein | 471 | 50% helix, 11% strand | A2A259 |
| A | Polycystic kidney disease protein 1-like 3 | protein | 446 | 48% helix, 12% 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 · 5 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.82 | 0.85 | 85 | empty |
| 2 | 675 | 0.82 | 0.86 | 76 | empty |
| 3 | 1005 | 0.81 | 0.82 | 113 | empty |
| 4 | 984 | 0.80 | 0.81 | 103 | CA |
| 5 | 686 | 0.78 | 0.82 | 74 | CA |
Interfaces
6 interfaces between chains.
- B–C · 3592 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 3472 Ų buried · 19 hydrogen bonds · protein-protein
- C–A · 2917 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 2867 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 124 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 7D7F · Structure of PKD1L3-CTD/PKD2L1 in calcium-bound 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 0.86
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 7D7F · PDBe 7D7F · UniProt A2A259 · UniProt Q2EG98
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