MolNFT v1 · #153563 · protein
Human MTHFD2 in complex with compound 1
6JID · Bifunctional methylenetetrahydrofolate…: “Human MTHFD2 in complex with compound 1”. X-ray diffraction, 2 ligands (BQC, PO4), 5 pockets (best druggability 0.66). MolNFT v1 #153563 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6JID
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial
- EC
- 1.5.1.15, 3.5.4.9
- UniProt
- P13995
- Ligands
- BQC, PO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 294 | 39% helix, 16% strand | P13995 |
| B | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 289 | 42% helix, 15% strand | P13995 |
Ligands and binding sites
- BQC · 5-(4-oxo-2-phenyl-1,5,7,8-tetrahydropyrido[4,3-d]pyrimidine-6(4H)-carbonyl)-1,3-dihydro-2H-2lambda~6~,1-benzothiazole-2,2-dione · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.66 | 0.78 | 44 | BQC |
| 2 | 475 | 0.65 | 0.77 | 55 | BQC, PO4, GOL |
| 3 | 178 | 0.45 | 0.75 | 28 | PO4, GOL |
| 4 | 106 | 0.39 | 0.75 | 24 | empty |
| 5 | 100 | 0.39 | 0.75 | 17 | GOL |
Interfaces
1 interface between chains.
- A–B · 1572 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
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 P13995
- Elsewhere: RCSB PDB 6JID · PDBe 6JID · UniProt P13995
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