MolNFT v1 · #51908 · protein
Structure of unliganded arylmalonate decarboxylase
2VLB: “Structure of unliganded arylmalonate decarboxylase”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.71). MolNFT v1 #51908 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VLB
- Type
- protein
- Length
- 918 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arylmalonate decarboxylase
- EC
- 4.1.1.76
- UniProt
- Q05115
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 235 | 47% helix, 17% strand | Q05115 |
| B | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 217 | 47% helix, 18% strand | Q05115 |
| C | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 236 | 48% helix, 16% strand | Q05115 |
| D | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 230 | 48% helix, 17% strand | Q05115 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, D, C
- BME · Beta-mercaptoethanol · additive · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.71 | 0.82 | 47 | BME |
| 2 | 106 | 0.61 | 0.88 | 25 | PO4, EDO |
| 3 | 248 | 0.56 | 0.77 | 40 | BME |
| 4 | 171 | 0.50 | 0.78 | 29 | empty |
| 5 | 138 | 0.47 | 0.78 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–D · 785 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 719 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 385 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 368 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 175 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (additive adduct).
Compared structures
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 Q05115
- Elsewhere: RCSB PDB 2VLB · PDBe 2VLB · UniProt Q05115
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