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Crystal structure of 2-methylisocitrate lyase (prpb) from salmonella enterica serovar typhimurium
Analyse Crystal structure of 2-methylisocitrate lyase (prpb) from salmonella enterica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UJQ
- Type
- protein
- Length
- 1,083 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
- Q56062
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 272 | 53% helix, 14% strand | Q56062 |
| B | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 268 | 53% helix, 14% strand | Q56062 |
| C | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 275 | 53% helix, 13% strand | Q56062 |
| D | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 268 | 50% helix, 14% strand | Q56062 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.87 | 0.90 | 94 | empty |
| 2 | 316 | 0.68 | 0.82 | 46 | empty |
| 3 | 168 | 0.66 | 0.86 | 39 | empty |
| 4 | 245 | 0.66 | 0.83 | 38 | empty |
| 5 | 145 | 0.65 | 0.87 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3474 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 3322 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 607 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 567 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 460 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1UJQ · Crystal structure of 2-methylisocitrate lyase (PrpB) from Salmonella enterica serovar… · the same entry in another collection · chain D against D, TM-score 1.00
- Q56062 · AlphaFold monomer V2.0 prediction for 2-methylisocitrate lyase (Q56062) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q56062
- Elsewhere: RCSB PDB 1UJQ · PDBe 1UJQ · UniProt Q56062
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