Research workbench
Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase
Analyse Linkage between the bacterial acid stress and stringent responses: the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q16
- Type
- protein
- Length
- 3,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine decarboxylase, inducible
- EC
- 4.1.1.18
- UniProt
- P0A9H3
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Lysine decarboxylase, inducible (EC 4.1.1.18) | protein | 711 | 39% helix, 17% strand | P0A9H3 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.79 | 0.81 | 90 | empty |
| 2 | 893 | 0.78 | 0.81 | 86 | empty |
| 3 | 1150 | 0.77 | 0.79 | 99 | empty |
| 4 | 732 | 0.76 | 0.81 | 85 | empty |
| 5 | 1168 | 0.76 | 0.79 | 97 | empty |
Interfaces
5 interfaces between chains.
- C–E · 1501 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 1478 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1468 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1458 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1438 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (cofactor).
Compared structures
- 3Q16 · Linkage between the Bacterial Acid Stress and Stringent Responses: The Structure of the… · the same entry in another collection · chain E against E, TM-score 1.00
- P0A9H3 · AlphaFold monomer V2.0 prediction for inducible lysine decarboxylase (P0A9H3) · a predicted model of the same protein · 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 P0A9H3
- Elsewhere: RCSB PDB 3Q16 · PDBe 3Q16 · UniProt P0A9H3
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