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Crystal structure of the C123S 2-methylisocitrate lyase mutant from escherichia COLI in complex with the reaction product, MG(II)- pyruvate and succinate
Analyse Crystal structure of the C123S 2-methylisocitrate lyase mutant from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XG3
- Type
- protein
- Length
- 1,144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable methylisocitrate lyase
- EC
- 4.1.3.30
- UniProt
- P77541
- Ligands
- PYR, MG
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 288 | 51% helix, 13% strand | P77541 |
| B | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 286 | 51% helix, 13% strand | P77541 |
| C | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 287 | 51% helix, 13% strand | P77541 |
| D | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 283 | 51% helix, 13% strand | P77541 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.85 | 0.90 | 72 | empty |
| 2 | 101 | 0.77 | 0.98 | 30 | PYR, SIN |
| 3 | 97 | 0.77 | 0.98 | 30 | MG, PYR, SIN |
| 4 | 97 | 0.77 | 0.98 | 29 | MG, PYR, SIN |
| 5 | 402 | 0.76 | 0.86 | 40 | MG, PYR |
Interfaces
6 interfaces between chains.
- A–B · 3941 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 3773 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 758 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 715 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 656 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1XG3 · Crystal structure of the C123S 2-methylisocitrate lyase mutant from Escherichia coli in… · the same entry in another collection · chain D against D, TM-score 1.00
- P77541 · AlphaFold monomer V2.0 prediction for 2-methylisocitrate lyase (P77541) · a predicted model of the same protein · chain B 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 P77541
- Elsewhere: RCSB PDB 1XG3 · PDBe 1XG3 · UniProt P77541
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