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Crystal structure of DELTA516-525 human cystathionine beta-synthase D444N mutant containing C-terminal 6XHIS tag
Analyse Crystal structure of DELTA516-525 human cystathionine beta-synthase D444N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L28
- Type
- protein
- Length
- 1,971 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-synthase
- EC
- 4.2.1.22
- UniProt
- P35520
- Ligands
- PLP, HEM
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 493 | 38% helix, 18% strand | P35520 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 494 | 38% helix, 17% strand | P35520 |
| C | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 491 | 38% helix, 18% strand | P35520 |
| D | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 493 | 38% helix, 18% strand | P35520 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.81 | 0.98 | 20 | empty |
| 2 | 132 | 0.80 | 0.98 | 20 | empty |
| 3 | 82 | 0.76 | 0.98 | 31 | PLP |
| 4 | 539 | 0.74 | 0.82 | 53 | empty |
| 5 | 77 | 0.74 | 0.97 | 31 | PLP |
Interfaces
6 interfaces between chains.
- A–C · 3861 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 3856 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 155 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 134 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 102 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4L28 · Crystal structure of delta516-525 human cystathionine beta-synthase D444N mutant… · the same entry in another collection · chain D against D, TM-score 1.00
- P35520 · AlphaFold monomer V2.0 prediction for cystathionine beta-synthase (P35520) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 P35520
- Elsewhere: RCSB PDB 4L28 · PDBe 4L28 · UniProt P35520
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