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Crystal structure of ipm isomerase large subunit from methanococcus jannaschii (MJ0499)
Analyse Crystal structure of ipm isomerase large subunit from methanococcus jannaschii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KP1
- Type
- protein
- Length
- 423 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ISOPROPYLMALATE/CITRAMALATE isomerase large subunit
- EC
- 4.2.1.33, 4.2.1.35
- UniProt
- P81291
- Ligands
- KP1, MG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ISOPROPYLMALATE/CITRAMALATE isomerase large subunit (EC 4.2.1.33, 4.2.1.35) | protein | 423 | 38% helix, 20% strand | P81291 |
Ligands and binding sites
- KP1 · 2,4-dimethylpentane-2,4-diol · ligand · chains A
- MG · Magnesium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.71 | 0.86 | 39 | KP1, MPD |
| 2 | 143 | 0.45 | 0.76 | 20 | empty |
| 3 | 96 | 0.42 | 0.78 | 23 | empty |
| 4 | 96 | 0.39 | 0.77 | 27 | empty |
| 5 | 51 | 0.36 | 0.80 | 12 | empty |
Modifications
Observed in the structure: 13 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4KP1 · Crystal structure of IPM isomerase large subunit from methanococcus jannaschii (MJ0499) · the same entry in another collection · chain A against A, TM-score 1.00
- P81291 · AlphaFold monomer V2.0 prediction for ISOPROPYLMALATE/CITRAMALATE isomerase large subunit… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P81291
- Elsewhere: RCSB PDB 4KP1 · PDBe 4KP1 · UniProt P81291
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