Research workbench
Crystal structure of the holo forms of rhodotorula graminis D- mandelate dehydrogenase at 2.5A.
Analyse Crystal structure of the holo forms of rhodotorula graminis D- mandelate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W2L
- Type
- protein
- Length
- 1,380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-mandelate dehydrogenase
- UniProt
- Q7LLW9
- Ligands
- NAD, SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-mandelate dehydrogenase | protein | 346 | 40% helix, 16% strand | Q7LLW9 |
| B | D-mandelate dehydrogenase | protein | 345 | 42% helix, 16% strand | Q7LLW9 |
| C | D-mandelate dehydrogenase | protein | 344 | 41% helix, 16% strand | Q7LLW9 |
| D | D-mandelate dehydrogenase | protein | 345 | 41% helix, 16% strand | Q7LLW9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.75 | 0.78 | 89 | NAD, SO4 |
| 2 | 729 | 0.74 | 0.79 | 70 | NAD, SO4 |
| 3 | 694 | 0.74 | 0.80 | 69 | NAD, SO4 |
| 4 | 674 | 0.72 | 0.79 | 67 | NAD, SO4 |
| 5 | 242 | 0.50 | 0.75 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2716 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 2668 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 252 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2W2L · Crystal structure of the holo forms of Rhodotorula graminis D- mandelate dehydrogenase at… · 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 Q7LLW9
- Elsewhere: RCSB PDB 2W2L · PDBe 2W2L · UniProt Q7LLW9
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