MolNFT v1 · #171988 · protein
Maeb full-length acetyl-CoA bound state
6ZNG · NADP-dependent malate DEHYDROGENASE,MALATE dehydrogenase: “Maeb full-length acetyl-CoA bound state”. X-ray diffraction, 1 ligand (ACO), 20 pockets (best druggability 0.83). MolNFT v1 #171988 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ZNG
- Type
- protein
- Length
- 4,501 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent malate DEHYDROGENASE,MALATE dehydrogenase
- EC
- 1.1.1.40
- UniProt
- Q6MM14, Q6MM15
- Ligands
- ACO
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADP-dependent malate DEHYDROGENASE,MALATE dehydrogenase (EC 1.1.1.40) | protein | 749 | 47% helix, 14% strand | Q6MM14, Q6MM15 |
| B | NADP-dependent malate DEHYDROGENASE,MALATE dehydrogenase (EC 1.1.1.40) | protein | 748 | 48% helix, 14% strand | Q6MM14, Q6MM15 |
| C | NADP-dependent malate DEHYDROGENASE,MALATE dehydrogenase (EC 1.1.1.40) | protein | 750 | 48% helix, 15% strand | Q6MM14, Q6MM15 |
| D | NADP-dependent malate DEHYDROGENASE,MALATE dehydrogenase (EC 1.1.1.40) | protein | 750 | 48% helix, 14% strand | Q6MM14, Q6MM15 |
| E | NADP-dependent malate DEHYDROGENASE,MALATE dehydrogenase (EC 1.1.1.40) | protein | 751 | 47% helix, 15% strand | Q6MM14, Q6MM15 |
| F | NADP-dependent malate DEHYDROGENASE,MALATE dehydrogenase (EC 1.1.1.40) | protein | 753 | 48% helix, 15% strand | Q6MM14, Q6MM15 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.83 | 0.84 | 103 | empty |
| 2 | 1039 | 0.82 | 0.83 | 83 | empty |
| 3 | 1009 | 0.81 | 0.83 | 86 | empty |
| 4 | 1031 | 0.80 | 0.82 | 121 | empty |
| 5 | 1043 | 0.80 | 0.82 | 115 | empty |
Interfaces
12 interfaces between chains.
- A–B · 6505 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 6342 Ų buried · 67 hydrogen bonds · protein-protein
- E–F · 6340 Ų buried · 72 hydrogen bonds · protein-protein
- C–F · 653 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 592 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6ZNG · MaeB full-length acetyl-CoA bound state · 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 Q6MM14
- Every structure of UniProt Q6MM15
- Elsewhere: RCSB PDB 6ZNG · PDBe 6ZNG · UniProt Q6MM14 · UniProt Q6MM15
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