MolNFT v1 · #121523 · protein
Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of toblerone fold enzymes
5HY4 · Ring-opening amidohydrolase: “Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of toblerone…”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #121523 on GenesisL1…
- PDB
- 5HY4
- Type
- protein
- Length
- 2,769 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ring-opening amidohydrolase
- EC
- 3.5.2.15
- UniProt
- E3JD18
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 361 | 33% helix, 26% strand | E3JD18 |
| B | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 360 | 33% helix, 29% strand | E3JD18 |
| C | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 348 | 32% helix, 27% strand | E3JD18 |
| D | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 333 | 32% helix, 30% strand | E3JD18 |
| E | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 349 | 34% helix, 27% strand | E3JD18 |
| F | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 350 | 34% helix, 27% strand | E3JD18 |
| G | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 340 | 34% helix, 24% strand | E3JD18 |
| H | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 328 | 32% helix, 30% strand | E3JD18 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.84 | 0.93 | 38 | empty |
| 2 | 359 | 0.84 | 0.93 | 38 | empty |
| 3 | 381 | 0.84 | 0.93 | 39 | empty |
| 4 | 359 | 0.83 | 0.93 | 37 | empty |
| 5 | 922 | 0.79 | 0.82 | 127 | empty |
Interfaces
14 interfaces between chains.
- A–C · 1501 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1495 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 1494 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1487 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 425 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5HY4 · Structure-function analysis of functionally diverse members of the cyclic amide hydrolase… · the same entry in another collection · chain H against H, TM-score 1.00
- E3JD18 · AlphaFold monomer V2.0 prediction for cyclic amide hydrolase (E3JD18) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 E3JD18
- Elsewhere: RCSB PDB 5HY4 · PDBe 5HY4 · UniProt E3JD18
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