MolNFT v1 · #68602 · protein
Structure of the pterin-binding domain metr of 5- methyltetrahydrofolate-homocysteine methyltransferase from bacteroides thetaiotaomicron
3K13 · 5-methyltetrahydrofolate-homocysteine methyltransferase: “Structure of the pterin-binding domain metr of 5- methyltetrahydrofolate-homocysteine methyltransferase from…”. X-ray diffraction, 3 ligands (THH, NA, K), 9 pockets (best…
- PDB
- 3K13
- Type
- protein
- Length
- 859 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methyltetrahydrofolate-homocysteine methyltransferase
- UniProt
- Q8ABD0
- Ligands
- THH, NA, K
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5-methyltetrahydrofolate-homocysteine methyltransferase | protein | 286 | 53% helix, 15% strand | Q8ABD0 |
| C | 5-methyltetrahydrofolate-homocysteine methyltransferase | protein | 287 | 54% helix, 15% strand | Q8ABD0 |
Ligands and binding sites
- THH · N-[4-({[(6S)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 5 copies · chains A, B, C
- K · Potassium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.80 | 0.84 | 85 | GOL |
| 2 | 620 | 0.67 | 0.76 | 62 | GOL, THH |
| 3 | 566 | 0.66 | 0.77 | 61 | THH, GOL, K |
| 4 | 649 | 0.66 | 0.75 | 64 | GOL, THH |
| 5 | 79 | 0.43 | 0.80 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 855 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3K13 · Structure of the pterin-binding domain MeTr of 5-methyltetrahydrofolate-homocysteine… · the same entry in another collection · chain B against B, 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 Q8ABD0
- Elsewhere: RCSB PDB 3K13 · PDBe 3K13 · UniProt Q8ABD0
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