Research workbench
Crystal structure of N-terminally tagged apo-ubid from E. COLI
Analyse Crystal structure of N-terminally tagged apo-ubid from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M1C
- Type
- protein
- Length
- 1,345 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
- EC
- 4.1.1.98
- UniProt
- P0AAB5
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.98) | protein | 437 | 28% helix, 29% strand | P0AAB5 |
| B | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.98) | protein | 460 | 31% helix, 28% strand | P0AAB5 |
| C | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.98) | protein | 448 | 32% helix, 27% strand | P0AAB5 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.81 | 0.82 | 76 | PG4 |
| 2 | 104 | 0.81 | 0.98 | 19 | empty |
| 3 | 1137 | 0.79 | 0.81 | 81 | empty |
| 4 | 982 | 0.77 | 0.79 | 88 | empty |
| 5 | 107 | 0.42 | 0.77 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4215 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 1224 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5M1C · Crystal structure of N-terminally tagged apo-UbiD from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
- P0AAB5 · AlphaFold monomer V2.0 prediction for 3-octaprenyl-4-hydroxybenzoate carboxy-lyase… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P0AAB5
- Elsewhere: RCSB PDB 5M1C · PDBe 5M1C · UniProt P0AAB5
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