Research workbench
X-ray crystal structure of a serine hydroxymethyltransferase from burkholderia cenocepacia with covalently attached pyridoxal phosphate
Analyse X-ray crystal structure of a serine hydroxymethyltransferase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N0W
- Type
- protein
- Length
- 1,659 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- B4ECY9
- Ligands
- PLP, SO4
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 416 | 50% helix, 13% strand | B4ECY9 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 414 | 50% helix, 14% strand | B4ECY9 |
| C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 415 | 50% helix, 13% strand | B4ECY9 |
| D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 414 | 50% helix, 14% strand | B4ECY9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.71 | 0.84 | 46 | PLP, SO4 |
| 2 | 65 | 0.70 | 0.97 | 30 | PLP |
| 3 | 60 | 0.70 | 0.97 | 25 | PLP |
| 4 | 368 | 0.69 | 0.81 | 29 | SO4 |
| 5 | 399 | 0.67 | 0.80 | 29 | SO4 |
Interfaces
5 interfaces between chains.
- A–C · 4473 Ų buried · 65 hydrogen bonds · protein-protein
- B–D · 4252 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 65 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4N0W · X-ray crystal structure of a serine hydroxymethyltransferase from Burkholderia… · 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 B4ECY9
- Elsewhere: RCSB PDB 4N0W · PDBe 4N0W · UniProt B4ECY9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.