MolNFT v1 · #140629 · protein
The structure of DRFAM20C1
5YH0: “The structure of DRFAM20C1”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #140629 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YH0
- Type
- protein
- Length
- 4,594 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DRFAM20C1
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 11 distinct chains · 35% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DRFAM20C1 | protein | 386 | 35% helix, 12% strand | — |
| B | DRFAM20C1 | protein | 380 | 36% helix, 13% strand | — |
| C | DRFAM20C1 | protein | 390 | 33% helix, 13% strand | — |
| D | DRFAM20C1 | protein | 382 | 35% helix, 12% strand | — |
| E | DRFAM20C1 | protein | 385 | 35% helix, 13% strand | — |
| F | DRFAM20C1 | protein | 377 | 35% helix, 13% strand | — |
| G | DRFAM20C1 | protein | 386 | 34% helix, 12% strand | — |
| H | DRFAM20C1 | protein | 380 | 35% helix, 12% strand | — |
| I | DRFAM20C1 | protein | 383 | 35% helix, 13% strand | — |
| J, L | DRFAM20C1 | protein | 378 | 37% helix, 12% strand | — |
| K | DRFAM20C1 | protein | 389 | 34% helix, 12% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.84 | 0.85 | 107 | empty |
| 2 | 844 | 0.82 | 0.84 | 81 | empty |
| 3 | 847 | 0.81 | 0.84 | 92 | empty |
| 4 | 1159 | 0.80 | 0.82 | 92 | empty |
| 5 | 689 | 0.80 | 0.84 | 78 | empty |
Interfaces
16 interfaces between chains.
- C–D · 957 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 954 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 954 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 948 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 disulfide (disulfide).
Compared structures
- 5YH0 · The structure of DrFam20C1 · 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
- Elsewhere: RCSB PDB 5YH0 · PDBe 5YH0
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