MolNFT v1 · #62139 · protein
Putative 5-carboxymethyl-2-hydroxymuconate isomerase from pseudomonas aeruginosa.
3E6Q: “Putative 5-carboxymethyl-2-hydroxymuconate isomerase from pseudomonas aeruginosa.”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.84). MolNFT v1 #62139 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3E6Q
- Type
- protein
- Length
- 1,520 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 5-carboxymethyl-2-hydroxymuconate isomerase
- UniProt
- Q9I2D8
- Ligands
- NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, G, H, I | Putative 5-carboxymethyl-2-hydroxymuconate isomerase | protein | 126 | 30% helix, 37% strand | Q9I2D8 |
| D | Putative 5-carboxymethyl-2-hydroxymuconate isomerase | protein | 128 | 30% helix, 38% strand | Q9I2D8 |
| E, J, K, L | Putative 5-carboxymethyl-2-hydroxymuconate isomerase | protein | 127 | 30% helix, 38% strand | Q9I2D8 |
| F | Putative 5-carboxymethyl-2-hydroxymuconate isomerase | protein | 128 | 30% helix, 38% strand | Q9I2D8 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, F, G, H
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- FMT · Formic acid · additive · 15 copies · chains A, B, L, F, E, H, G, I
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ACT · Acetate ion · additive · 2 copies · chains A, D, E, F
- IMD · Imidazole · additive · 2 copies · chains J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.84 | 0.89 | 48 | EDO, ACT, NA |
| 2 | 630 | 0.83 | 0.88 | 52 | EDO, NA, GOL, FMT |
| 3 | 643 | 0.83 | 0.88 | 49 | EDO, IMD |
| 4 | 631 | 0.83 | 0.88 | 52 | FMT, NA, GOL, EDO |
| 5 | 292 | 0.56 | 0.76 | 26 | empty |
Interfaces
16 interfaces between chains.
- J–L · 1413 Ų buried · 43 hydrogen bonds · protein-protein
- G–I · 1412 Ų buried · 43 hydrogen bonds · protein-protein
- D–F · 1406 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 1404 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 1404 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3E6Q · Putative 5-carboxymethyl-2-hydroxymuconate isomerase from Pseudomonas aeruginosa. · the same entry in another collection · chain I against I, 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 Q9I2D8
- Elsewhere: RCSB PDB 3E6Q · PDBe 3E6Q · UniProt Q9I2D8
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