Research workbench
X-ray crystal structure of a serine hydroxymethyl transferase in apo form from burkholderia cenocepacia
Analyse X-ray crystal structure of a serine hydroxymethyl transferase in apo form from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MSO
- Type
- protein
- Length
- 765 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- B4ECY9
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 383 | 51% helix, 14% strand | B4ECY9 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 382 | 51% helix, 14% strand | B4ECY9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.62 | 0.75 | 69 | PO4 |
| 2 | 273 | 0.59 | 0.79 | 40 | empty |
| 3 | 358 | 0.58 | 0.76 | 52 | PO4 |
| 4 | 121 | 0.47 | 0.79 | 15 | empty |
| 5 | 121 | 0.38 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3105 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 4MSO · X-ray crystal structure of a serine hydroxymethyl transferase in apo form from… · 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 4MSO · PDBe 4MSO · UniProt B4ECY9
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