Research workbench
Crystal structure of carbon sulfoxide lyase, EGT2 Y134F with sulfenic acid intermediate
Analyse Crystal structure of carbon sulfoxide lyase, EGT2 Y134F with sulfenic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V12
- Type
- protein
- Length
- 3,502 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EGT2
- EC
- 4.4.1.-
- UniProt
- A7UX13
- Ligands
- 8QJ
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | EGT2 (EC 4.4.1.-) | protein | 436 | 45% helix, 15% strand | A7UX13 |
| G | EGT2 (EC 4.4.1.-) | protein | 441 | 45% helix, 15% strand | A7UX13 |
| F | EGT2 (EC 4.4.1.-) | protein | 440 | 46% helix, 15% strand | A7UX13 |
| H | EGT2 (EC 4.4.1.-) | protein | 435 | 44% helix, 15% strand | A7UX13 |
| C | EGT2 (EC 4.4.1.-) | protein | 436 | 44% helix, 15% strand | A7UX13 |
| D | EGT2 (EC 4.4.1.-) | protein | 438 | 46% helix, 15% strand | A7UX13 |
| A | EGT2 (EC 4.4.1.-) | protein | 439 | 45% helix, 15% strand | A7UX13 |
| B | EGT2 (EC 4.4.1.-) | protein | 437 | 45% helix, 16% strand | A7UX13 |
Ligands and binding sites
- 8QJ · (2~{S})-3-(2-oxidanylsulfanyl-1~{H}-imidazol-4-yl)-2-(trimethyl-$L^{4}-azanyl)propanoic acid · ligand · 2 copies · chains E, F, A, B
- FMT · Formic acid · additive · 8 copies · chains E, G, F, H, C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.84 | 0.96 | 48 | empty |
| 2 | 1059 | 0.84 | 0.85 | 102 | empty |
| 3 | 650 | 0.79 | 0.84 | 87 | FMT |
| 4 | 584 | 0.79 | 0.85 | 79 | FMT |
| 5 | 556 | 0.78 | 0.84 | 82 | empty |
Interfaces
11 interfaces between chains.
- G–H · 3225 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3200 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3163 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 3037 Ų buried · 49 hydrogen bonds · protein-protein
- F–D · 287 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (cofactor, nonstandard).
Compared structures
- 5V12 · Crystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulfenic acid intermediate · the same entry in another collection · chain B against B, TM-score 1.00
- A7UX13 · AlphaFold monomer V2.0 prediction for hercynylcysteine sulfoxide lyase (A7UX13) · a predicted model of the same protein · chain E 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 A7UX13
- Elsewhere: RCSB PDB 5V12 · PDBe 5V12 · UniProt A7UX13
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