Research workbench
Crystal structure of R. rubrum transhydrogenase domain I with bound NADH
Analyse Crystal structure of R. rubrum transhydrogenase domain I with bound NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L7E
- Type
- protein
- Length
- 1,449 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide nucleotide transhydrogenase, subunit alpha 1
- EC
- 1.6.1.1
- UniProt
- Q60164
- Ligands
- NAI
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide nucleotide transhydrogenase, subunit alpha 1 (EC 1.6.1.1) | protein | 372 | 37% helix, 19% strand | Q60164 |
| B | Nicotinamide nucleotide transhydrogenase, subunit alpha 1 (EC 1.6.1.1) | protein | 357 | 38% helix, 19% strand | Q60164 |
| C | Nicotinamide nucleotide transhydrogenase, subunit alpha 1 (EC 1.6.1.1) | protein | 353 | 37% helix, 20% strand | Q60164 |
| D | Nicotinamide nucleotide transhydrogenase, subunit alpha 1 (EC 1.6.1.1) | protein | 367 | 38% helix, 19% strand | Q60164 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.77 | 0.80 | 75 | NAI |
| 2 | 992 | 0.76 | 0.79 | 89 | NAI |
| 3 | 810 | 0.74 | 0.79 | 74 | empty |
| 4 | 672 | 0.71 | 0.78 | 60 | empty |
| 5 | 591 | 0.68 | 0.77 | 46 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1824 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1727 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 651 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 111 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1L7E · Crystal Structure of R. rubrum Transhydrogenase Domain I with Bound NADH · 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 Q60164
- Elsewhere: RCSB PDB 1L7E · PDBe 1L7E · UniProt Q60164
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