Research workbench
Structure of penicillin-binding protein a from M. tuberculosis: imipenem acyl-enzyme complex
Analyse Structure of penicillin-binding protein a from M. tuberculosis: imipenem… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UPN
- Type
- protein
- Length
- 871 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein a
- EC
- 3.4.16.4
- UniProt
- P71586
- Ligands
- IM2
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein a (EC 3.4.16.4) | protein | 435 | 34% helix, 22% strand | P71586 |
| B | Penicillin-binding protein a (EC 3.4.16.4) | protein | 436 | 37% helix, 22% strand | P71586 |
Ligands and binding sites
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.76 | 0.79 | 101 | IM2 |
| 2 | 82 | 0.70 | 0.95 | 23 | empty |
| 3 | 67 | 0.70 | 0.96 | 22 | empty |
| 4 | 180 | 0.46 | 0.75 | 29 | empty |
| 5 | 98 | 0.44 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 451 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3UPN · Structure of penicillin-binding protein A from M. tuberculosis: imipenem acyl-enzyme… · 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 P71586
- Elsewhere: RCSB PDB 3UPN · PDBe 3UPN · UniProt P71586
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