MolNFT v1 · #164654 · protein
Crystal structure of 2-methylisocitrate lyase (prpb) from pseudomonas aeruginosa in apo form.
6T4V: “Crystal structure of 2-methylisocitrate lyase (prpb) from pseudomonas aeruginosa in apo form.”. X-ray diffraction, 1 ligand (PYR), 8 pockets (best druggability 0.84). MolNFT v1 #164654 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6T4V
- Type
- protein
- Length
- 1,106 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-methylisocitrate lyase
- EC
- 4.1.3.30
- UniProt
- Q9I5E2
- Ligands
- PYR
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B | 2-methylisocitrate lyase (EC 4.1.3.30) | protein | 277 | 53% helix, 14% strand | Q9I5E2 |
| A, D | 2-methylisocitrate lyase (EC 4.1.3.30) | protein | 276 | 53% helix, 14% strand | Q9I5E2 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.84 | 0.86 | 128 | PYR |
| 2 | 959 | 0.74 | 0.77 | 96 | empty |
| 3 | 928 | 0.74 | 0.77 | 98 | empty |
| 4 | 278 | 0.64 | 0.82 | 41 | empty |
| 5 | 196 | 0.62 | 0.83 | 33 | empty |
Interfaces
6 interfaces between chains.
- C–B · 3476 Ų buried · 54 hydrogen bonds · protein-protein
- A–D · 3435 Ų buried · 49 hydrogen bonds · protein-protein
- C–A · 959 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 945 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 469 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6T4V · Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in apo… · the same entry in another collection · chain C against C, 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 Q9I5E2
- Elsewhere: RCSB PDB 6T4V · PDBe 6T4V · UniProt Q9I5E2
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