Research workbench
Structure of human MTHFD2 in complex with TH9028
Analyse Structure of human MTHFD2 in complex with TH9028 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S4A
- Type
- protein
- Length
- 591 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
- KUK, NAD, PO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% 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 | 296 | 42% helix, 17% strand | P13995 |
| B | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 295 | 42% helix, 17% strand | P13995 |
Ligands and binding sites
- KUK · (2~{S})-2-[[5-[[2,4-bis(azanyl)-6-oxidanylidene-5~{H}-pyrimidin-5-yl]carbamoylamino]pyridin-2-yl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl) butanoic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.75 | 1.00 | 14 | empty |
| 2 | 645 | 0.70 | 0.78 | 62 | KUK, PO4, NAD |
| 3 | 622 | 0.69 | 0.77 | 61 | MPD, KUK, NAD |
| 4 | 97 | 0.37 | 0.75 | 20 | PO4, NAD |
| 5 | 77 | 0.35 | 0.76 | 15 | PO4, NAD |
Interfaces
1 interface between chains.
- A–B · 1622 Ų buried · 30 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 6S4A · PDBe 6S4A · UniProt P13995
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