Research workbench
Cryo-EM structure of NADH reduced form of NAD+-dependent formate dehydrogenase from rhodobacter capsulatus
Analyse Cryo-EM structure of NADH reduced form of NAD+-dependent formate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TG9
- Type
- protein
- Length
- 3,318 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase subunit alpha; Formate dehydrogenase subunit beta; Formate…
- EC
- 1.2.1.2
- UniProt
- A0A0E2PAE3, A0A0E2P9P2, A0A0E2PAI9, A0A0E2P9Z0
- Ligands
- SF4, MGD, FES, FMN, NAI, 6MO, H2S
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Formate dehydrogenase subunit alpha | protein | 949 | 29% helix, 14% strand | A0A0E2PAE3 |
| B, F | Formate dehydrogenase subunit beta | protein | 493 | 42% helix, 14% strand | A0A0E2P9P2 |
| G, C | Formate dehydrogenase subunit gamma (EC 1.2.1.2) | protein | 148 | 45% helix, 9% strand | A0A0E2PAI9 |
| D, H | NAD-dependent formate dehydrogenase subunit delta | protein | 69 | 67% helix, 0% strand | A0A0E2P9Z0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 10 copies · chains A, E, B, F
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 4 copies · chains A, E
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B, G, E, F, C
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, F
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B, E, F
- 6MO · Molybdenum(vi) ion · metal · 2 copies · chains A, E
- H2S · Hydrosulfuric acid · ion · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.89 | 0.95 | 85 | MGD, 6MO, H2S |
| 2 | 601 | 0.89 | 0.94 | 87 | MGD, 6MO, H2S |
| 3 | 1076 | 0.80 | 0.82 | 130 | empty |
| 4 | 873 | 0.78 | 0.81 | 79 | FMN, NAI |
| 5 | 845 | 0.76 | 0.80 | 68 | FMN, NAI |
Interfaces
9 interfaces between chains.
- B–G · 1808 Ų buried · 19 hydrogen bonds · protein-protein
- F–C · 1803 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1452 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1451 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1381 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6TG9 · Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from… · 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 A0A0E2PAE3
- Every structure of UniProt A0A0E2P9P2
- Every structure of UniProt A0A0E2PAI9
- Every structure of UniProt A0A0E2P9Z0
- Elsewhere: RCSB PDB 6TG9 · PDBe 6TG9 · UniProt A0A0E2PAE3 · UniProt A0A0E2P9P2 · UniProt A0A0E2PAI9 · UniProt A0A0E2P9Z0
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