MolNFT v1 · #154150 · protein
Engineered form of a putative cystathionine gamma-lyase
6K1M: “Engineered form of a putative cystathionine gamma-lyase”. X-ray diffraction, 2 ligands (PLP, PYR), 20 pockets (best druggability 0.74). MolNFT v1 #154150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K1M
- Type
- protein
- Length
- 1,528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-lyase
- EC
- 4.4.1.1
- UniProt
- B4SII9
- Ligands
- PLP, PYR
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 382 | 39% helix, 17% strand | B4SII9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.74 | 0.99 | 30 | empty |
| 2 | 71 | 0.74 | 0.98 | 32 | empty |
| 3 | 397 | 0.72 | 0.83 | 53 | PLP |
| 4 | 203 | 0.69 | 0.86 | 38 | PLP, PYR |
| 5 | 190 | 0.68 | 0.86 | 41 | PLP, PYR |
Interfaces
6 interfaces between chains.
- C–D · 2578 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2549 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 1550 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1424 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 956 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6K1M · Engineered 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 6K1M · PDBe 6K1M · UniProt B4SII9
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