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Structural basis for light acitvation of a chloroplast enzyme. the structure of sorghum NADP-malate dehydrogenase in its oxidized form
Analyse Structural basis for light acitvation of a chloroplast enzyme. the structure of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MDH
- Type
- protein
- Length
- 1,415 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (malate dehydrogenase)
- EC
- 1.1.1.82
- UniProt
- P17606
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (malate dehydrogenase) (EC 1.1.1.82) | protein | 351 | 43% helix, 17% strand | P17606 |
| B | Protein (malate dehydrogenase) (EC 1.1.1.82) | protein | 360 | 42% helix, 16% strand | P17606 |
| C | Protein (malate dehydrogenase) (EC 1.1.1.82) | protein | 352 | 41% helix, 17% strand | P17606 |
| D | Protein (malate dehydrogenase) (EC 1.1.1.82) | protein | 352 | 43% helix, 16% strand | P17606 |
Ligands and binding sites
- ZN · Zinc ion · metal · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.78 | 0.80 | 104 | ZN |
| 2 | 611 | 0.67 | 0.77 | 69 | empty |
| 3 | 534 | 0.67 | 0.77 | 55 | ZN |
| 4 | 583 | 0.66 | 0.77 | 67 | empty |
| 5 | 316 | 0.66 | 0.81 | 39 | ZN |
Interfaces
4 interfaces between chains.
- C–D · 2347 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2342 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 528 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 107 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7MDH · Structural basis for light acitvation of a chloroplast enzyme. the structure of sorghum… · the same entry in another collection · chain D against D, TM-score 1.00
- P17606 · AlphaFold monomer V2.0 prediction for malate dehydrogenase [NADP] 1, chloroplastic… · a predicted model of the same protein · 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 P17606
- Elsewhere: RCSB PDB 7MDH · PDBe 7MDH · UniProt P17606
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