Research workbench
Crystal structure of methanogen 3-isopropylmalate isomerase small subunit
Analyse Crystal structure of methanogen 3-isopropylmalate isomerase small subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VBA
- Type
- protein
- Length
- 997 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ISOPROPYLMALATE/CITRAMALATE isomerase small subunit
- EC
- 4.2.1.33, 4.2.1.35, 4.2.1.31
- UniProt
- Q58673
- Pockets
- 13 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ISOPROPYLMALATE/CITRAMALATE isomerase small subunit (EC 4.2.1.33, 4.2.1.35, 4.2.1.31) | protein | 169 | 34% helix, 21% strand | Q58673 |
| C | ISOPROPYLMALATE/CITRAMALATE isomerase small subunit (EC 4.2.1.33, 4.2.1.35, 4.2.1.31) | protein | 166 | 34% helix, 21% strand | Q58673 |
| D | ISOPROPYLMALATE/CITRAMALATE isomerase small subunit (EC 4.2.1.33, 4.2.1.35, 4.2.1.31) | protein | 163 | 35% helix, 21% strand | Q58673 |
| E, F | ISOPROPYLMALATE/CITRAMALATE isomerase small subunit (EC 4.2.1.33, 4.2.1.35, 4.2.1.31) | protein | 165 | 34% helix, 21% strand | Q58673 |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.66 | 0.87 | 29 | empty |
| 2 | 251 | 0.62 | 0.81 | 37 | empty |
| 3 | 176 | 0.53 | 0.79 | 34 | empty |
| 4 | 117 | 0.49 | 0.80 | 24 | empty |
| 5 | 162 | 0.46 | 0.76 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1287 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 944 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 797 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 298 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 297 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3VBA · Crystal structure of methanogen 3-isopropylmalate isomerase small subunit · the same entry in another collection · chain F against F, TM-score 1.00
- Q58673 · AlphaFold monomer V2.0 prediction for ISOPROPYLMALATE/CITRAMALATE isomerase small subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q58673
- Elsewhere: RCSB PDB 3VBA · PDBe 3VBA · UniProt Q58673
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.