Research workbench
Ergothioneine-biosynthetic ntn hydrolase egtc with glutamine
Analyse Ergothioneine-biosynthetic ntn hydrolase egtc with glutamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZFK
- Type
- protein
- Length
- 916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase egtc
- EC
- 3.5.1.-
- UniProt
- A0R5M9
- Ligands
- GLN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amidohydrolase egtc (EC 3.5.1.-) | protein | 227 | 24% helix, 34% strand | A0R5M9 |
| B | Amidohydrolase egtc (EC 3.5.1.-) | protein | 231 | 23% helix, 33% strand | A0R5M9 |
| C | Amidohydrolase egtc (EC 3.5.1.-) | protein | 230 | 23% helix, 33% strand | A0R5M9 |
| D | Amidohydrolase egtc (EC 3.5.1.-) | protein | 228 | 24% helix, 34% strand | A0R5M9 |
Ligands and binding sites
- GLN · Glutamine · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.83 | 0.84 | 90 | EDO |
| 2 | 105 | 0.60 | 0.87 | 22 | empty |
| 3 | 166 | 0.59 | 0.83 | 41 | GLN |
| 4 | 103 | 0.56 | 0.85 | 22 | empty |
| 5 | 138 | 0.44 | 0.76 | 24 | GLN |
Interfaces
6 interfaces between chains.
- C–D · 540 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 536 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 374 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 360 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 359 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ZFK · Ergothioneine-biosynthetic Ntn hydrolase EgtC with glutamine · the same entry in another collection · chain D against D, TM-score 1.00
- A0R5M9 · AlphaFold monomer V2.0 prediction for gamma-glutamyl-hercynylcysteine sulfoxide hydrolase… · a predicted model of the same protein · chain A 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 4ZFK · PDBe 4ZFK · UniProt A0R5M9
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