Research workbench
Crystal structure of NADH-dependent reductase A1-R' complexed with NAD
Analyse Crystal structure of NADH-dependent reductase A1-R' complexed with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TKM
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-dependent reductase for 4-deoxy-L-erythro-5- hexoseulose uronate
- Ligands
- NAD, SO4
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-dependent reductase for 4-deoxy-L-erythro-5- hexoseulose uronate | protein | 242 | 48% helix, 15% strand | — |
| B | NADH-dependent reductase for 4-deoxy-L-erythro-5- hexoseulose uronate | protein | 241 | 50% helix, 16% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.51 | 0.76 | 39 | SO4 |
| 2 | 248 | 0.50 | 0.75 | 43 | NAD |
| 3 | 51 | 0.45 | 0.84 | 14 | empty |
| 4 | 52 | 0.43 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1578 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4TKM · Crystal structure of NADH-dependent reductase A1-R' complexed with NAD · 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
- Elsewhere: RCSB PDB 4TKM · PDBe 4TKM
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