MolNFT v1 · #112242 · protein
Ergothioneine-biosynthetic ntn hydrolase egtc, apo form
4ZFJ · Amidohydrolase egtc: “Ergothioneine-biosynthetic ntn hydrolase egtc, apo form”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #112242 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZFJ
- Type
- protein
- Length
- 2,732 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase egtc
- EC
- 3.5.1.-
- UniProt
- A0R5M9
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Amidohydrolase egtc (EC 3.5.1.-) | protein | 229 | 24% helix, 34% strand | A0R5M9 |
| B, E, I | Amidohydrolase egtc (EC 3.5.1.-) | protein | 228 | 23% helix, 33% strand | A0R5M9 |
| D, G, K, L | Amidohydrolase egtc (EC 3.5.1.-) | protein | 227 | 23% helix, 35% strand | A0R5M9 |
| F | Amidohydrolase egtc (EC 3.5.1.-) | protein | 230 | 23% helix, 33% strand | A0R5M9 |
| H, J | Amidohydrolase egtc (EC 3.5.1.-) | protein | 226 | 24% helix, 34% strand | A0R5M9 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 12 copies · chains A, C, B, D, E, K, F, L, G, I, H, J
- XPE · 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol · additive · 11 copies · chains A, B, C, D, E, H, J, F, G, L, K, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.84 | 0.86 | 104 | XPE |
| 2 | 1113 | 0.84 | 0.85 | 118 | MES, XPE |
| 3 | 1155 | 0.82 | 0.84 | 122 | XPE, MES |
| 4 | 592 | 0.78 | 0.84 | 86 | empty |
| 5 | 106 | 0.60 | 0.87 | 22 | empty |
Interfaces
22 interfaces between chains.
- H–K · 616 Ų buried · 10 hydrogen bonds · protein-protein
- G–L · 584 Ų buried · 9 hydrogen bonds · protein-protein
- F–I · 580 Ų buried · 9 hydrogen bonds · protein-protein
- E–J · 576 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 558 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- A0R5M9 · AlphaFold monomer V2.0 prediction for gamma-glutamyl-hercynylcysteine sulfoxide hydrolase… · a predicted model of the same protein · chain H 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 A0R5M9
- Elsewhere: RCSB PDB 4ZFJ · PDBe 4ZFJ · UniProt A0R5M9
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