Research workbench
Helicobacter pylori serine hydroxymethyl transferase in apo form
Analyse Helicobacter pylori serine hydroxymethyl transferase in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F93
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- P56089
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 387 | 47% helix, 14% strand | P56089 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 385 | 48% helix, 14% strand | P56089 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.69 | 0.82 | 56 | empty |
| 2 | 227 | 0.47 | 0.74 | 35 | empty |
| 3 | 181 | 0.47 | 0.74 | 18 | empty |
| 4 | 210 | 0.45 | 0.73 | 33 | empty |
| 5 | 105 | 0.36 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2492 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6F93 · Helicobacter pylori serine hydroxymethyl transferase in apo form · the same entry in another collection · chain A against A, TM-score 1.00
- P56089 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (P56089) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P56089
- Elsewhere: RCSB PDB 6F93 · PDBe 6F93 · UniProt P56089
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