Research workbench
Structure of NAD+-bound leucine dehydrogenase from geobacillus stearothermophilus by cryo-EM
Analyse Structure of NAD+-bound leucine dehydrogenase from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ACH
- Type
- protein
- Length
- 2,912 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine dehydrogenase
- UniProt
- A0A0K2HC96
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Leucine dehydrogenase | protein | 364 | 41% helix, 16% strand | A0A0K2HC96 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 944 | 0.87 | 0.89 | 121 | empty |
| 2 | 1080 | 0.87 | 0.88 | 119 | empty |
| 3 | 1055 | 0.86 | 0.88 | 122 | empty |
| 4 | 1178 | 0.86 | 0.87 | 141 | empty |
| 5 | 630 | 0.69 | 0.78 | 49 | NAD |
Interfaces
16 interfaces between chains.
- C–D · 1335 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1335 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1335 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1334 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1259 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6ACH · Structure of NAD+-bound leucine dehydrogenase from Geobacillus stearothermophilus by… · 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 A0A0K2HC96
- Elsewhere: RCSB PDB 6ACH · PDBe 6ACH · UniProt A0A0K2HC96
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