MolNFT v1 · #153561 · protein
Human MTHFD2 in complex with DS44960156
6JIB · Bifunctional methylenetetrahydrofolate…: “Human MTHFD2 in complex with DS44960156”. X-ray diffraction, 2 ligands (BQF, PO4), 5 pockets (best druggability 0.71). MolNFT v1 #153561 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6JIB
- Type
- protein
- Length
- 587 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
- BQF, PO4
- Pockets
- 5 · best druggability 0.71
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 | 293 | 40% helix, 17% strand | P13995 |
| B | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 294 | 41% helix, 16% strand | P13995 |
Ligands and binding sites
- BQF · 4-(5-oxo-1,5-dihydro-2H-[1]benzopyrano[3,4-c]pyridine-3(4H)-carbonyl)benzoic acid · ligand · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 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 | 642 | 0.71 | 0.78 | 72 | BQF, PO4, GOL |
| 2 | 505 | 0.69 | 0.79 | 55 | BQF, GOL |
| 3 | 100 | 0.39 | 0.75 | 20 | empty |
| 4 | 104 | 0.39 | 0.75 | 19 | empty |
| 5 | 59 | 0.31 | 0.76 | 16 | PO4, BQF |
Interfaces
1 interface between chains.
- A–B · 1608 Ų buried · 28 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 6JIB · PDBe 6JIB · UniProt P13995
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