MolNFT v1 · #136724 · protein
Carbon sulfoxide lyase, EGT2 Y134F in complex with its substrate
5V1X · Hercynylcysteine sulfoxide lyase: “Carbon sulfoxide lyase, EGT2 Y134F in complex with its substrate”. X-ray diffraction, 1 ligand (8VV), 20 pockets (best druggability 0.84). MolNFT v1 #136724 on GenesisL1: 3D structure, binding…
- PDB
- 5V1X
- Type
- protein
- Length
- 3,513 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hercynylcysteine sulfoxide lyase
- EC
- 4.4.1.-
- UniProt
- A7UX13
- Ligands
- 8VV
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Hercynylcysteine sulfoxide lyase (EC 4.4.1.-) | protein | 438 | 45% helix, 15% strand | A7UX13 |
| F, B | Hercynylcysteine sulfoxide lyase (EC 4.4.1.-) | protein | 436 | 45% helix, 14% strand | A7UX13 |
| D | Hercynylcysteine sulfoxide lyase (EC 4.4.1.-) | protein | 447 | 45% helix, 15% strand | A7UX13 |
| C, H | Hercynylcysteine sulfoxide lyase (EC 4.4.1.-) | protein | 438 | 44% helix, 14% strand | A7UX13 |
| A | Hercynylcysteine sulfoxide lyase (EC 4.4.1.-) | protein | 439 | 46% helix, 15% strand | A7UX13 |
| G | Hercynylcysteine sulfoxide lyase (EC 4.4.1.-) | protein | 441 | 45% helix, 14% strand | A7UX13 |
Ligands and binding sites
- 8VV · (2~{S})-3-[2-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfinyl-1~{H}-imidazol-4-yl]-2-(trimethyl-$L^{4}-azanyl)propanoic acid · ligand · 2 copies · chains D, C, A, B
- FMT · Formic acid · additive · 5 copies · chains E, F, D, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.84 | 0.85 | 111 | empty |
| 2 | 222 | 0.83 | 0.96 | 47 | empty |
| 3 | 246 | 0.83 | 0.95 | 53 | empty |
| 4 | 219 | 0.83 | 0.96 | 43 | empty |
| 5 | 570 | 0.80 | 0.86 | 79 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3298 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 3235 Ų buried · 56 hydrogen bonds · protein-protein
- D–C · 3199 Ų buried · 48 hydrogen bonds · protein-protein
- G–H · 3183 Ų buried · 51 hydrogen bonds · protein-protein
- E–A · 311 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (cofactor).
Compared structures
- 5V1X · Carbon Sulfoxide lyase, Egt2 Y134F in complex with its substrate · the same entry in another collection · chain H against H, 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 5V1X · PDBe 5V1X · UniProt A7UX13
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