Research workbench
Structure of uroporphyrinogen decarboxylase from acinetobacter baumannii
Analyse Structure of uroporphyrinogen decarboxylase from acinetobacter baumannii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZR8
- Type
- protein
- Length
- 707 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uroporphyrinogen decarboxylase
- EC
- 4.1.1.37
- UniProt
- A0A0A2T261
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uroporphyrinogen decarboxylase (EC 4.1.1.37) | protein | 353 | 50% helix, 13% strand | A0A0A2T261 |
| B | Uroporphyrinogen decarboxylase (EC 4.1.1.37) | protein | 354 | 51% helix, 13% strand | A0A0A2T261 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.83 | 0.84 | 91 | EDO, CL |
| 2 | 453 | 0.76 | 0.84 | 48 | EDO, CL |
| 3 | 158 | 0.61 | 0.84 | 23 | empty |
| 4 | 157 | 0.58 | 0.82 | 24 | empty |
| 5 | 167 | 0.46 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1361 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4ZR8 · Structure of uroporphyrinogen decarboxylase from Acinetobacter baumannii · 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 A0A0A2T261
- Elsewhere: RCSB PDB 4ZR8 · PDBe 4ZR8 · UniProt A0A0A2T261
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