Research workbench
X-ray crystal structure of a serine hydroxymethyltransferase with covalently bound plp from rickettsia rickettsii str. sheila smith
Analyse X-ray crystal structure of a serine hydroxymethyltransferase with covalently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J5U
- Type
- protein
- Length
- 840 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- A8GTI9
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 420 | 50% helix, 13% strand | A8GTI9 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.72 | 0.83 | 44 | empty |
| 2 | 384 | 0.70 | 0.82 | 40 | empty |
| 3 | 234 | 0.49 | 0.74 | 28 | empty |
| 4 | 122 | 0.48 | 0.79 | 22 | empty |
| 5 | 115 | 0.46 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4531 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 4J5U · X-ray crystal structure of a serine hydroxymethyltransferase with covalently bound PLP… · the same entry in another collection · chain A against A, TM-score 1.00
- A8GTI9 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (A8GTI9) · a predicted model of the same protein · chain A 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 A8GTI9
- Elsewhere: RCSB PDB 4J5U · PDBe 4J5U · UniProt A8GTI9
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