Research workbench
Ergothioneine-biosynthetic ntn hydrolase variant EGTC_C2A with natural substrate
Analyse Ergothioneine-biosynthetic ntn hydrolase variant EGTC_C2A with natural substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZFL
- Type
- protein
- Length
- 2,743 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase egtc
- EC
- 3.5.1.-
- UniProt
- A0R5M9
- Ligands
- 4NK
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G, H, I, J | Amidohydrolase egtc (EC 3.5.1.-) | protein | 229 | 24% helix, 34% strand | A0R5M9 |
| C, K | Amidohydrolase egtc (EC 3.5.1.-) | protein | 228 | 24% helix, 33% strand | A0R5M9 |
| D, L | Amidohydrolase egtc (EC 3.5.1.-) | protein | 227 | 24% helix, 34% strand | A0R5M9 |
| F | Amidohydrolase egtc (EC 3.5.1.-) | protein | 230 | 24% helix, 34% strand | A0R5M9 |
Ligands and binding sites
- 4NK · (1S)-1-carboxy-4-({(1R)-1-carboxy-2-[(S)-{4-[(2S)-2-carboxy-2-(trimethylammonio)ethyl]-1H-imidazol-2-yl}sulfinyl]ethyl}amino)-4-oxobutan-1-aminium · ligand · 12 copies · chains A, C, B, D, E, K, F, L, G, I, H, J
- GOL · Glycerol · additive · 4 copies · chains E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1083 | 0.85 | 0.86 | 128 | empty |
| 2 | 984 | 0.84 | 0.86 | 113 | empty |
| 3 | 1133 | 0.83 | 0.84 | 125 | empty |
| 4 | 519 | 0.76 | 0.84 | 73 | empty |
| 5 | 240 | 0.66 | 0.83 | 34 | 4NK |
Interfaces
22 interfaces between chains.
- A–C · 677 Ų buried · 4 hydrogen bonds · protein-protein
- H–J · 671 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 666 Ų buried · 3 hydrogen bonds · protein-protein
- G–I · 662 Ų buried · 4 hydrogen bonds · protein-protein
- E–K · 659 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- A0R5M9 · AlphaFold monomer V2.0 prediction for gamma-glutamyl-hercynylcysteine sulfoxide hydrolase… · a predicted model of the same protein · chain L against A, TM-score 0.99
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 4ZFL · PDBe 4ZFL · UniProt A0R5M9
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