Research workbench
Crystal structure of human cystathionine gamma lyase with S-3- carboxpropyl-L-cysteine
Analyse Crystal structure of human cystathionine gamma lyase with S-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NBA
- Type
- protein
- Length
- 1,557 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
- P32929
- Ligands
- P1T
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 389 | 38% helix, 17% strand | P32929 |
| C | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 390 | 38% helix, 17% strand | P32929 |
Ligands and binding sites
- P1T · 2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]acrylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.80 | 0.98 | 20 | empty |
| 2 | 96 | 0.77 | 0.98 | 26 | P1T |
| 3 | 100 | 0.77 | 0.98 | 24 | P1T |
| 4 | 95 | 0.76 | 0.97 | 25 | P1T |
| 5 | 93 | 0.76 | 0.97 | 26 | P1T |
Interfaces
6 interfaces between chains.
- A–B · 2530 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2530 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1490 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1472 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 955 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6NBA · Crystal structure of Human Cystathionine gamma lyase with S-3-Carboxpropyl-L-Cysteine · the same entry in another collection · chain D against D, TM-score 1.00
- P32929 · AlphaFold monomer V2.0 prediction for cystathionine gamma-lyase (P32929) · a predicted model of the same protein · chain C 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 P32929
- Elsewhere: RCSB PDB 6NBA · PDBe 6NBA · UniProt P32929
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