MolNFT v1 · #137042 · protein
Crystal structure of a serine hydroxymethyltransferase from helicobacter pylori
5VC2: “Crystal structure of a serine hydroxymethyltransferase from helicobacter pylori”. X-ray diffraction, 6 pockets (best druggability 0.66). MolNFT v1 #137042 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VC2
- Type
- protein
- Length
- 766 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- B5Z9V7
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 386 | 47% helix, 15% strand | B5Z9V7 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 380 | 49% helix, 14% strand | B5Z9V7 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.66 | 0.78 | 81 | empty |
| 2 | 61 | 0.41 | 0.80 | 15 | empty |
| 3 | 101 | 0.37 | 0.74 | 20 | empty |
| 4 | 89 | 0.33 | 0.73 | 15 | empty |
| 5 | 53 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2473 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 5VC2 · Crystal structure of a serine hydroxymethyltransferase from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- B5Z9V7 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (B5Z9V7) · 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 B5Z9V7
- Elsewhere: RCSB PDB 5VC2 · PDBe 5VC2 · UniProt B5Z9V7
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