Research workbench
Crystal structure of agrobacterium tumefaciens malate dehydrogenase, new york structural genomics consortium
Analyse Crystal structure of agrobacterium tumefaciens malate dehydrogenase, new york… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z2I
- Type
- protein
- Length
- 1,400 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- UniProt
- Q7CRW4
- Ligands
- NAD
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malate dehydrogenase | protein | 350 | 43% helix, 17% strand | Q7CRW4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.84 | 0.85 | 107 | NAD |
| 2 | 908 | 0.84 | 0.85 | 87 | NAD |
| 3 | 120 | 0.82 | 0.98 | 21 | empty |
| 4 | 121 | 0.81 | 0.97 | 22 | empty |
| 5 | 768 | 0.78 | 0.82 | 76 | NAD |
Interfaces
3 interfaces between chains.
- C–D · 3299 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3293 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1042 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1Z2I · CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL… · 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 Q7CRW4
- Elsewhere: RCSB PDB 1Z2I · PDBe 1Z2I · UniProt Q7CRW4
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