MolNFT v1 · #136696 · protein
Crystal structure of carbon sulfoxide lyase, EGT2 Y134F with sulfenic acid intermediate
5V12: “Crystal structure of carbon sulfoxide lyase, EGT2 Y134F with sulfenic acid intermediate”. X-ray diffraction, 1 ligand (8QJ), 20 pockets (best druggability 0.84). MolNFT v1 #136696 on GenesisL1: 3D structure, binding sites and…
- 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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