MolNFT v1 · #9919 · protein
Crystal structure of R153C E. COLI malate dehydrogenase
1IB6: “Crystal structure of R153C E. COLI malate dehydrogenase”. X-ray diffraction, 2 ligands (NAD, SO4), 12 pockets (best druggability 0.79). MolNFT v1 #9919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IB6
- Type
- protein
- Length
- 1,248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P61889
- Ligands
- NAD, SO4
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 312 | 46% helix, 17% strand | P61889 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.79 | 0.84 | 111 | SO4, NAD |
| 2 | 341 | 0.71 | 0.84 | 72 | SO4, NAD |
| 3 | 229 | 0.71 | 0.87 | 48 | SO4, NAD |
| 4 | 186 | 0.46 | 0.75 | 33 | empty |
| 5 | 166 | 0.41 | 0.73 | 30 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1505 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1494 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 294 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 269 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P61889
- Elsewhere: RCSB PDB 1IB6 · PDBe 1IB6 · UniProt P61889
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