MolNFT v1 · #117124 · protein
Abyu - wildtype
5DYV · Yd repeat-containing protein: “Abyu - wildtype”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #117124 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DYV
- Type
- protein
- Length
- 1,055 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yd repeat-containing protein
- UniProt
- F4F7G1
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yd repeat-containing protein | protein | 135 | 6% helix, 62% strand | F4F7G1 |
| B | Yd repeat-containing protein | protein | 133 | 6% helix, 64% strand | F4F7G1 |
| C, D | Yd repeat-containing protein | protein | 134 | 6% helix, 63% strand | F4F7G1 |
| E, F, G | Yd repeat-containing protein | protein | 130 | 6% helix, 65% strand | F4F7G1 |
| H | Yd repeat-containing protein | protein | 129 | 6% helix, 64% strand | F4F7G1 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.83 | 0.97 | 24 | EPE |
| 2 | 181 | 0.82 | 0.97 | 27 | EPE |
| 3 | 175 | 0.82 | 0.97 | 25 | EPE |
| 4 | 179 | 0.82 | 0.96 | 27 | EPE |
| 5 | 123 | 0.80 | 0.97 | 24 | EPE |
Interfaces
8 interfaces between chains.
- C–E · 869 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 866 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 862 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 821 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DYV · AbyU - wildtype · 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 F4F7G1
- Elsewhere: RCSB PDB 5DYV · PDBe 5DYV · UniProt F4F7G1
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