Research workbench
Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form
Analyse Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FA3
- Type
- protein
- Length
- 4,795 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Aspergillus niger
- Molecule
- 2,3-dimethylmalate lyase
- EC
- 4.1.3.32
- UniProt
- Q2L887
- Ligands
- OAF, MN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.6 · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H, O, P | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 301 | 46% helix, 12% strand | Q2L887 |
| B | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 302 | 46% helix, 12% strand | Q2L887 |
| I, K, M | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 300 | 47% helix, 12% strand | Q2L887 |
| J, N | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 292 | 48% helix, 13% strand | Q2L887 |
| L | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 300 | 47% helix, 13% strand | Q2L887 |
Ligands and binding sites
- OAF · 2,2-difluoro-3,3-dihydroxybutanedioic acid · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, K, L, M, O, P
- MN · Manganese (II) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- GOL · Glycerol · additive · 5 copies · chains A, B, C, I, E, G, H, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.88 | 0.90 | 133 | GOL |
| 2 | 970 | 0.88 | 0.90 | 144 | GOL |
| 3 | 832 | 0.87 | 0.90 | 123 | empty |
| 4 | 728 | 0.86 | 0.90 | 100 | empty |
| 5 | 1003 | 0.77 | 0.79 | 98 | empty |
Interfaces
34 interfaces between chains.
- C–D · 3536 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 3520 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 3508 Ų buried · 34 hydrogen bonds · protein-protein
- O–P · 3499 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3480 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3FA3 · Crystal structure of 2,3-dimethylmalate lyase, a pep MUTASE/ISOCITRATE lyase superfamily… · the same entry in another collection · chain A against A, 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 Q2L887
- Elsewhere: RCSB PDB 3FA3 · PDBe 3FA3 · UniProt Q2L887
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