MolNFT v1 · #66070 · protein
Crystal structure of 4-methylmuconolactone methylisomerase (H52A) in complex with 4-methylmuconolactone
3HFK: “Crystal structure of 4-methylmuconolactone methylisomerase (H52A) in complex with 4-methylmuconolactone”. X-ray diffraction, 1 ligand (4ML), 11 pockets (best druggability 0.73). MolNFT v1 #66070 on GenesisL1: 3D structure, binding…
- PDB
- 3HFK
- Type
- protein
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-methylmuconolactone methylisomerase
- EC
- 5.4.99.14
- UniProt
- C5MR76
- Ligands
- 4ML
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-methylmuconolactone methylisomerase (EC 5.4.99.14) | protein | 115 | 36% helix, 30% strand | C5MR76 |
| B | 4-methylmuconolactone methylisomerase (EC 5.4.99.14) | protein | 116 | 38% helix, 29% strand | C5MR76 |
| C | 4-methylmuconolactone methylisomerase (EC 5.4.99.14) | protein | 109 | 33% helix, 31% strand | C5MR76 |
| D | 4-methylmuconolactone methylisomerase (EC 5.4.99.14) | protein | 108 | 33% helix, 31% strand | C5MR76 |
Ligands and binding sites
- 4ML · [(2S)-2-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid · ligand · 7 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.73 | 0.99 | 15 | 4ML |
| 2 | 51 | 0.71 | 0.98 | 15 | 4ML |
| 3 | 158 | 0.67 | 0.87 | 26 | 4ML |
| 4 | 176 | 0.67 | 0.86 | 26 | 4ML |
| 5 | 234 | 0.57 | 0.79 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2142 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2125 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 206 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HFK · Crystal structure of 4-methylmuconolactone methylisomerase (H52A) in complex with… · the same entry in another collection · chain B against B, 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 C5MR76
- Elsewhere: RCSB PDB 3HFK · PDBe 3HFK · UniProt C5MR76
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