Research workbench
Activation of catalytic cysteine without a base in a mutant penicillin acylase precursor
Analyse Activation of catalytic cysteine without a base in a mutant penicillin acylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MJI
- Type
- protein
- Length
- 1,334 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin acylase
- EC
- 3.5.1.11
- UniProt
- P12256
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Penicillin acylase (EC 3.5.1.11) | protein | 334 | 19% helix, 33% strand | P12256 |
| C, D | Penicillin acylase (EC 3.5.1.11) | protein | 333 | 19% helix, 31% strand | P12256 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.85 | 0.93 | 75 | empty |
| 2 | 154 | 0.82 | 0.98 | 39 | empty |
| 3 | 107 | 0.78 | 0.98 | 35 | empty |
| 4 | 94 | 0.74 | 0.95 | 23 | empty |
| 5 | 85 | 0.71 | 0.93 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3267 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 3220 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1267 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1256 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 393 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3MJI · Activation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor · the same entry in another collection · chain A against A, TM-score 1.00
- P12256 · AlphaFold monomer V2.0 prediction for penicillin acylase (P12256) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P12256
- Elsewhere: RCSB PDB 3MJI · PDBe 3MJI · UniProt P12256
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