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Crystal structure of formate dehydrogenase FDH2 D222Q/Q223R mutant enzyme from granulicella mallensis MP5ACTX8 in complex with NADP and azide.
Analyse Crystal structure of formate dehydrogenase FDH2 D222Q/Q223R mutant enzyme from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T9X
- Type
- protein
- Length
- 1,532 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
- 19 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Formate dehydrogenase (EC 1.17.1.9) | protein | 383 | 36% helix, 17% strand | G8NTI5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains B, A, C, D
- AZI · Azide ion · ion · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.80 | 0.84 | 80 | AZI, NAP |
| 2 | 307 | 0.75 | 0.87 | 42 | AZI, NAP |
| 3 | 486 | 0.74 | 0.83 | 77 | empty |
| 4 | 408 | 0.73 | 0.83 | 57 | AZI, NAP |
| 5 | 385 | 0.72 | 0.84 | 56 | AZI, NAP |
Interfaces
6 interfaces between chains.
- B–A · 3800 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 736 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 291 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 120 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6T9X · Crystal structure of formate dehydrogenase FDH2 D222Q/Q223R mutant enzyme from… · 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 G8NTI5
- Elsewhere: RCSB PDB 6T9X · PDBe 6T9X · UniProt G8NTI5
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