Research workbench
Crystal structure of methylthioalkylmalate synthase (BJUMAM1.1) from brassica juncea
Analyse Crystal structure of methylthioalkylmalate synthase (BJUMAM1.1) from brassica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E1J
- Type
- protein
- Length
- 817 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-isopropylmalate synthase, a genome specific 1
- UniProt
- C5J4P1
- Ligands
- KMT, COA, MN
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-isopropylmalate synthase, a genome specific 1 | protein | 409 | 49% helix, 14% strand | C5J4P1 |
| B | 2-isopropylmalate synthase, a genome specific 1 | protein | 408 | 49% helix, 13% strand | C5J4P1 |
Ligands and binding sites
- KMT · 4-(methylsulfanyl)-2-oxobutanoic acid · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.78 | 0.99 | 29 | empty |
| 2 | 450 | 0.74 | 0.83 | 58 | COA, MN, KMT |
| 3 | 418 | 0.73 | 0.83 | 53 | KMT, COA |
| 4 | 137 | 0.48 | 0.78 | 20 | empty |
| 5 | 59 | 0.39 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3768 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 6E1J · Crystal Structure of Methylthioalkylmalate Synthase (BjuMAM1.1) from Brassica juncea · 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 C5J4P1
- Elsewhere: RCSB PDB 6E1J · PDBe 6E1J · UniProt C5J4P1
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