MolNFT v1 · #63452 · protein
Crystal structure of 2,3-dimethylmalate lyase, a pep MUTASE/ISOCITRATE lyase superfamily member, triclinic crystal form
3FA4: “Crystal structure of 2,3-dimethylmalate lyase, a pep MUTASE/ISOCITRATE lyase superfamily member, triclinic…”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.88). MolNFT v1 #63452 on GenesisL1: 3D structure…
- PDB
- 3FA4
- Type
- protein
- Length
- 3,407 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-dimethylmalate lyase
- EC
- 4.1.3.32
- UniProt
- Q2L887
- Ligands
- MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 11 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 284 | 49% helix, 13% strand | Q2L887 |
| B | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 288 | 49% helix, 13% strand | Q2L887 |
| C | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 284 | 50% helix, 13% strand | Q2L887 |
| D | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 284 | 50% helix, 13% strand | Q2L887 |
| E | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 286 | 50% helix, 13% strand | Q2L887 |
| F | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 285 | 49% helix, 13% strand | Q2L887 |
| H | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 282 | 50% helix, 13% strand | Q2L887 |
| I | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 282 | 50% helix, 13% strand | Q2L887 |
| J | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 280 | 51% helix, 13% strand | Q2L887 |
| K | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 280 | 51% helix, 13% strand | Q2L887 |
| L | 2,3-dimethylmalate lyase (EC 4.1.3.32) | protein | 288 | 49% helix, 13% strand | Q2L887 |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.88 | 0.90 | 206 | MG |
| 2 | 1162 | 0.88 | 0.89 | 153 | MG |
| 3 | 1070 | 0.83 | 0.84 | 129 | MG |
| 4 | 221 | 0.78 | 0.92 | 57 | MG |
| 5 | 1074 | 0.76 | 0.78 | 117 | MG |
Interfaces
23 interfaces between chains.
- K–L · 3153 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 3031 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2995 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2981 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2960 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3FA4 · 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 3FA4 · PDBe 3FA4 · UniProt Q2L887
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