Research workbench
Structure of the N318H variant of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HUDA in complex with FMN
Analyse Structure of the N318H variant of the reversible pyrrole-2-carboxylic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ABO
- Type
- protein
- Length
- 1,990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubid-like decarboxylase
- EC
- 4.1.1.-
- UniProt
- A0A5F1BUV8
- Ligands
- FMN, MN, NA
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 499 | 34% helix, 24% strand | A0A5F1BUV8 |
| B | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 496 | 33% helix, 24% strand | A0A5F1BUV8 |
| D | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 497 | 33% helix, 25% strand | A0A5F1BUV8 |
| A | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 498 | 34% helix, 24% strand | A0A5F1BUV8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains C, B, D, A
- MN · Manganese (II) ion · metal · 4 copies · chains C, B, D, A
- NA · Sodium ion · metal · 4 copies · chains C, B, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.80 | 0.99 | 22 | empty |
| 2 | 469 | 0.80 | 0.88 | 58 | FMN |
| 3 | 115 | 0.79 | 0.98 | 22 | empty |
| 4 | 535 | 0.79 | 0.85 | 55 | FMN, NA |
| 5 | 551 | 0.78 | 0.85 | 61 | FMN, NA |
Interfaces
6 interfaces between chains.
- C–B · 3729 Ų buried · 49 hydrogen bonds · protein-protein
- D–A · 3700 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 559 Ų buried · 4 hydrogen bonds · protein-protein
- C–A · 319 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7ABO · Structure of the N318H variant of the reversible pyrrole-2-carboxylic acid decarboxylase… · the same entry in another collection · chain C against C, 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 A0A5F1BUV8
- Elsewhere: RCSB PDB 7ABO · PDBe 7ABO · UniProt A0A5F1BUV8
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