Research workbench
Crystal structure of formate dehydrogenase FDH2 D222A/Q223R enzyme from granulicella mallensis MP5ACTX8 in complex with NADP and azide.
Analyse Crystal structure of formate dehydrogenase FDH2 D222A/Q223R enzyme from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T9W
- Type
- protein
- Length
- 1,523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- EC
- 1.17.1.9
- UniProt
- G8NTI5
- Ligands
- NAP, AZI
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Formate dehydrogenase (EC 1.17.1.9) | protein | 383 | 36% helix, 17% strand | G8NTI5 |
| D | Formate dehydrogenase (EC 1.17.1.9) | protein | 374 | 33% helix, 18% strand | G8NTI5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains B, A, C
- AZI · Azide ion · ion · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.83 | 0.84 | 118 | NAP, AZI |
| 2 | 669 | 0.75 | 0.81 | 80 | empty |
| 3 | 378 | 0.73 | 0.84 | 55 | NAP, AZI |
| 4 | 349 | 0.73 | 0.85 | 51 | NAP, AZI |
| 5 | 424 | 0.70 | 0.81 | 45 | empty |
Interfaces
4 interfaces between chains.
- A–D · 3903 Ų buried · 50 hydrogen bonds · protein-protein
- B–A · 748 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 308 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 132 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6T9W · Crystal structure of formate dehydrogenase FDH2 D222A/Q223R enzyme from Granulicella… · the same entry in another collection · chain A against A, 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 G8NTI5
- Elsewhere: RCSB PDB 6T9W · PDBe 6T9W · UniProt G8NTI5
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