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Structure of sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (shvdccd) in open form
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
- 7AE5
- Type
- protein
- Length
- 3,192 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
- RB, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 11 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 465 | 27% helix, 25% strand | Q9S4M7 |
| C | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 469 | 29% helix, 27% strand | Q9S4M7 |
| D | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 476 | 27% helix, 25% strand | Q9S4M7 |
| E | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 470 | 28% helix, 25% strand | Q9S4M7 |
| F | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 462 | 28% helix, 26% strand | Q9S4M7 |
| A | Phenolic acid decarboxylase (EC 4.1.1.63, 4.1.1.61) | protein | 466 | 27% helix, 25% strand | Q9S4M7 |
| b | Protein shdd | protein | 65 | 12% helix, 23% strand | Q4R102 |
| c, d | Protein shdd | protein | 67 | 12% helix, 22% strand | Q4R102 |
| e | Protein shdd | protein | 64 | 8% helix, 23% strand | Q4R102 |
| f | Protein shdd | protein | 58 | 5% helix, 26% strand | Q4R102 |
| a | Protein shdd | protein | 63 | 13% helix, 24% strand | Q4R102 |
Ligands and binding sites
- RB · Rubidium ion · metal · 12 copies · chains B, C, D, E, F, A
- ZN · Zinc ion · metal · 6 copies · chains b, c, d, e, f, a
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.82 | 0.84 | 105 | empty |
| 2 | 1188 | 0.80 | 0.82 | 110 | empty |
| 3 | 675 | 0.79 | 0.84 | 48 | empty |
| 4 | 80 | 0.79 | 0.99 | 22 | empty |
| 5 | 1158 | 0.78 | 0.80 | 96 | empty |
Interfaces
18 interfaces between chains.
- E–A · 4026 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 3902 Ų buried · 26 hydrogen bonds · protein-protein
- B–F · 3888 Ų buried · 27 hydrogen bonds · protein-protein
- C–c · 1610 Ų buried · 27 hydrogen bonds · protein-protein
- D–d · 1594 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7AE5 · Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in… · 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 Q9S4M7
- Every structure of UniProt Q4R102
- Elsewhere: RCSB PDB 7AE5 · PDBe 7AE5 · UniProt Q9S4M7 · UniProt Q4R102
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