MolNFT v1 · #127106 · protein
Human cystathionine beta-synthase (cbs) P.P49L DELTA409-551 variant
5MMS: “Human cystathionine beta-synthase (cbs) P.P49L DELTA409-551 variant”. X-ray diffraction, 3 ligands (HEM, PLP, NA), 20 pockets (best druggability 0.83). MolNFT v1 #127106 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MMS
- Type
- protein
- Length
- 2,077 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-synthase
- EC
- 4.2.1.22
- UniProt
- P35520
- Ligands
- HEM, PLP, NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 340 | 41% helix, 17% strand | P35520 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 348 | 39% helix, 16% strand | P35520 |
| C | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 343 | 40% helix, 16% strand | P35520 |
| D | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 356 | 39% helix, 16% strand | P35520 |
| E | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 349 | 40% helix, 17% strand | P35520 |
| F | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 341 | 40% helix, 16% strand | P35520 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, F, B, C, D, E
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 3 copies · chains D, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.83 | 0.86 | 74 | empty |
| 2 | 152 | 0.82 | 0.98 | 20 | empty |
| 3 | 150 | 0.82 | 0.98 | 20 | empty |
| 4 | 640 | 0.82 | 0.87 | 54 | empty |
| 5 | 1106 | 0.80 | 0.82 | 73 | NA |
Interfaces
11 interfaces between chains.
- D–E · 1966 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1955 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 609 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 571 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 524 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5MMS · Human cystathionine beta-synthase (CBS) p.P49L delta409-551 variant · the same entry in another collection · chain F against F, TM-score 1.00
- P35520 · AlphaFold monomer V2.0 prediction for cystathionine beta-synthase (P35520) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 5MMS · PDBe 5MMS · UniProt P35520
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