MolNFT v1 · #16665 · protein
Crystal structure of pyruvate and MG2+ bound 2- methylisocitrate lyase (prpb) from salmonella typhimurium
1O5Q · Probable methylisocitrate lyase: “Crystal structure of pyruvate and MG2+ bound 2- methylisocitrate lyase (prpb) from salmonella typhimurium”. X-ray diffraction, 2 ligands (PYR, MG), 7 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 1O5Q
- Type
- protein
- Length
- 1,082 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
- Ligands
- PYR, MG
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 271 | 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, 14% strand | Q56062 |
| D | Probable methylisocitrate lyase (EC 4.1.3.30) | protein | 268 | 51% helix, 14% strand | Q56062 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.87 | 0.90 | 95 | empty |
| 2 | 844 | 0.71 | 0.76 | 93 | empty |
| 3 | 822 | 0.71 | 0.77 | 80 | empty |
| 4 | 278 | 0.66 | 0.83 | 43 | MG, PYR |
| 5 | 204 | 0.65 | 0.84 | 33 | MG, PYR |
Interfaces
6 interfaces between chains.
- A–B · 3465 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3332 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 545 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 454 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1O5Q · Crystal Structure of Pyruvate and Mg2+ bound 2-methylisocitrate lyase (PrpB) from… · 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 1O5Q · PDBe 1O5Q · UniProt Q56062
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