MolNFT v1 · #146525 · protein
Human mitochondrial serine hydroxymethyltransferase 2
6DK3 · Serine hydroxymethyltransferase, mitochondrial: “Human mitochondrial serine hydroxymethyltransferase 2”. X-ray diffraction, 1 ligand (UNX), 7 pockets (best druggability 0.43). MolNFT v1 #146525 on GenesisL1: 3D structure, binding…
- PDB
- 6DK3
- Type
- protein
- Length
- 423 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase, mitochondrial
- EC
- 2.1.2.1
- UniProt
- P34897
- Ligands
- UNX
- Pockets
- 7 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 423 | 50% helix, 14% strand | P34897 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.43 | 0.75 | 20 | empty |
| 2 | 85 | 0.43 | 0.79 | 20 | empty |
| 3 | 54 | 0.37 | 0.80 | 16 | empty |
| 4 | 54 | 0.31 | 0.76 | 14 | empty |
| 5 | 57 | 0.30 | 0.76 | 22 | empty |
Compared structures
- 6DK3 · HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASe 2 · the same entry in another collection · chain A against A, TM-score 1.00
- P34897 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, mitochondrial… · 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 P34897
- Elsewhere: RCSB PDB 6DK3 · PDBe 6DK3 · UniProt P34897
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