MolNFT v1 · #141335 · protein
Malate dehydrogenase binds silver at C113
5Z3W: “Malate dehydrogenase binds silver at C113”. X-ray diffraction, 1 ligand (AG), 17 pockets (best druggability 0.56). MolNFT v1 #141335 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Z3W
- Type
- protein
- Length
- 1,200 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
- AG
- Pockets
- 17 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 300 | 48% helix, 19% strand | P61889 |
Ligands and binding sites
- AG · Silver ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.56 | 0.73 | 56 | empty |
| 2 | 227 | 0.51 | 0.76 | 35 | empty |
| 3 | 211 | 0.49 | 0.75 | 40 | empty |
| 4 | 211 | 0.49 | 0.75 | 33 | empty |
| 5 | 243 | 0.47 | 0.73 | 36 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1616 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1597 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 292 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 219 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 210 Ų buried · 3 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 5Z3W · PDBe 5Z3W · UniProt P61889
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