Research workbench
Sulfolactate dehydrogenase from methanocaldococcus jannaschii
Analyse Sulfolactate dehydrogenase from methanocaldococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X06
- Type
- protein
- Length
- 2,752 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-sulfolactate dehydrogenase
- EC
- 1.1.1.272
- UniProt
- Q58820
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | L-sulfolactate dehydrogenase (EC 1.1.1.272) | protein | 344 | 43% helix, 18% strand | Q58820 |
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 | 225 | 0.85 | 0.97 | 34 | empty |
| 2 | 223 | 0.85 | 0.96 | 36 | empty |
| 3 | 212 | 0.85 | 0.97 | 33 | empty |
| 4 | 222 | 0.85 | 0.96 | 34 | empty |
| 5 | 897 | 0.83 | 0.85 | 111 | empty |
Interfaces
18 interfaces between chains.
- G–H · 3268 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3227 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 3223 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 3211 Ų buried · 29 hydrogen bonds · protein-protein
- E–G · 1270 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 2X06 · Sulfolactate dehydrogenase from methanocaldococcus jannaschii · the same entry in another collection · chain H against H, TM-score 1.00
- Q58820 · AlphaFold monomer V2.0 prediction for L-sulfolactate dehydrogenase (Q58820) · a predicted model of the same protein · chain C 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 Q58820
- Elsewhere: RCSB PDB 2X06 · PDBe 2X06 · UniProt Q58820
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