Research workbench
Structure of sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (shvdccd) in open form, with truncated shvdcd (V59X)
Analyse Structure of sedimentibacter hydroxybenzoicus vanillic acid decarboxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AE7
- Type
- protein
- Length
- 3,146 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenolic acid decarboxylase; Protein shdd
- EC
- 4.1.1.63, 4.1.1.61
- UniProt
- Q9S4M7, Q4R102
- Ligands
- ZN, NA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 467 | 28% helix, 25% strand | Q9S4M7 |
| B | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 468 | 28% helix, 26% strand | Q9S4M7 |
| C | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 471 | 27% helix, 24% strand | Q9S4M7 |
| D | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 475 | 30% helix, 25% strand | Q9S4M7 |
| E | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 461 | 28% helix, 27% strand | Q9S4M7 |
| F | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 471 | 29% helix, 25% strand | Q9S4M7 |
| a, c, d, e, f | Protein shdd | protein | 57 | 14% helix, 25% strand | Q4R102 |
| b | Protein shdd | protein | 48 | 8% helix, 29% strand | Q4R102 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains a, b, c, d, e, f
- NA · Sodium ion · metal · 5 copies · chains A, C, B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.80 | 0.82 | 115 | NA |
| 2 | 1140 | 0.80 | 0.81 | 90 | empty |
| 3 | 1197 | 0.79 | 0.81 | 88 | empty |
| 4 | 85 | 0.78 | 0.98 | 20 | empty |
| 5 | 74 | 0.78 | 0.99 | 20 | empty |
Interfaces
18 interfaces between chains.
- E–F · 3826 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 3692 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 3664 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1314 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1275 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7AE7 · Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in… · the same entry in another collection · chain f against f, 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 Q9S4M7
- Every structure of UniProt Q4R102
- Elsewhere: RCSB PDB 7AE7 · PDBe 7AE7 · UniProt Q9S4M7 · UniProt Q4R102
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.