MolNFT v1 · #144887 · protein
Monoclinic form of malic enzyme from sorghum at 2 ångströms resolution
6C7N: “Monoclinic form of malic enzyme from sorghum at 2 ångströms resolution”. X-ray diffraction, 2 ligands (NAP, PYR), 20 pockets (best druggability 0.90). MolNFT v1 #144887 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6C7N
- Type
- protein
- Length
- 2,030 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malic enzyme
- UniProt
- Q84LQ5
- Ligands
- NAP, PYR
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malic enzyme | protein | 553 | 49% helix, 12% strand | Q84LQ5 |
| C | Malic enzyme | protein | 535 | 47% helix, 10% strand | Q84LQ5 |
| D | Malic enzyme | protein | 389 | 54% helix, 8% strand | Q84LQ5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- PYR · Pyruvic acid · ligand · 3 copies · chains B, A, C, D
- GOL · Glycerol · additive · 17 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · chains B
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 | 875 | 0.90 | 0.93 | 122 | GOL |
| 2 | 554 | 0.89 | 0.95 | 65 | PYR |
| 3 | 564 | 0.89 | 0.94 | 64 | PYR |
| 4 | 196 | 0.78 | 0.93 | 35 | GOL |
| 5 | 608 | 0.74 | 0.81 | 60 | NAP |
Interfaces
6 interfaces between chains.
- A–B · 2638 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2627 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1166 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1100 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 342 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6C7N · Monoclinic form of malic enzyme from sorghum at 2 angstroms resolution · 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 Q84LQ5
- Elsewhere: RCSB PDB 6C7N · PDBe 6C7N · UniProt Q84LQ5
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