MolNFT v1 · #91374 · protein
Crystal structure of treponema denticola trans-2-enoyl-CoA reductase in complex with NAD
4FBG · Putative reductase TDE_0597: “Crystal structure of treponema denticola trans-2-enoyl-CoA reductase in complex with NAD”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.85). MolNFT v1 #91374 on GenesisL1: 3D…
- PDB
- 4FBG
- Type
- protein
- Length
- 6,372 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative reductase TDE_0597
- EC
- 1.3.1.44
- UniProt
- Q73Q47
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H, I | Putative reductase TDE_0597 (EC 1.3.1.44) | protein | 399 | 41% helix, 16% strand | Q73Q47 |
| B, E, J, K, M, O | Putative reductase TDE_0597 (EC 1.3.1.44) | protein | 397 | 41% helix, 16% strand | Q73Q47 |
| D, L | Putative reductase TDE_0597 (EC 1.3.1.44) | protein | 401 | 41% helix, 15% strand | Q73Q47 |
| F, G, N, P | Putative reductase TDE_0597 (EC 1.3.1.44) | protein | 398 | 42% helix, 16% strand | Q73Q47 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, E, G, H, I, K, M, P
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 | 1099 | 0.85 | 0.86 | 89 | empty |
| 2 | 1078 | 0.84 | 0.85 | 86 | empty |
| 3 | 1176 | 0.84 | 0.85 | 103 | NAD |
| 4 | 1016 | 0.84 | 0.85 | 83 | empty |
| 5 | 1142 | 0.84 | 0.85 | 89 | empty |
Interfaces
35 interfaces between chains.
- J–L · 490 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 487 Ų buried · 9 hydrogen bonds · protein-protein
- I–N · 445 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 441 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 423 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 modified (engineered).
Compared structures
- Q73Q47 · AlphaFold monomer V2.0 prediction for trans-2-enoyl-CoA reductase [NADH] (Q73Q47) · a predicted model of the same protein · chain K against A, TM-score 0.99
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 Q73Q47
- Elsewhere: RCSB PDB 4FBG · PDBe 4FBG · UniProt Q73Q47
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