Research workbench
PLP-bound form of a putative cystathionine gamma-lyase
Analyse PLP-bound form of a putative cystathionine gamma-lyase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K1N
- Type
- protein
- Length
- 1,493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.26
- Source
- Stenotrophomonas maltophilia (strain R551-3)
- Molecule
- Cystathionine gamma-lyase
- EC
- 4.4.1.1
- UniProt
- B4SII9
- Ligands
- PLP
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.26 · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 370 | 40% helix, 17% strand | B4SII9 |
| B | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 378 | 39% helix, 17% strand | B4SII9 |
| C | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 371 | 39% helix, 17% strand | B4SII9 |
| D | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 374 | 40% helix, 17% strand | B4SII9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.86 | 0.87 | 130 | PLP |
| 2 | 856 | 0.83 | 0.86 | 124 | PLP |
| 3 | 148 | 0.58 | 0.83 | 27 | empty |
| 4 | 200 | 0.57 | 0.80 | 38 | empty |
| 5 | 169 | 0.56 | 0.81 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2341 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2292 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 1592 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1441 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 836 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6K1N · Plp-bound form of a putative cystathionine gamma-lyase · the same entry in another collection · chain A 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 B4SII9
- Elsewhere: RCSB PDB 6K1N · PDBe 6K1N · UniProt B4SII9
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