MolNFT v1 · #117250 · protein
Crystal structure of D-alanine carboxypeptidase ampc from mycobacterium smegmatis
5E2H · Beta-lactamase: “Crystal structure of D-alanine carboxypeptidase ampc from mycobacterium smegmatis”. X-ray diffraction, 1 ligand (CL), 8 pockets (best druggability 0.74). MolNFT v1 #117250 on GenesisL1: 3D structure, binding sites…
- PDB
- 5E2H
- Type
- protein
- Length
- 1,062 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0QZC8
- Ligands
- CL
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-lactamase (EC 3.5.2.6) | protein | 354 | 41% helix, 19% strand | A0QZC8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.74 | 0.85 | 41 | empty |
| 2 | 540 | 0.67 | 0.77 | 74 | empty |
| 3 | 362 | 0.60 | 0.77 | 40 | CL |
| 4 | 329 | 0.60 | 0.78 | 46 | CL |
| 5 | 342 | 0.60 | 0.77 | 45 | CL |
Interfaces
2 interfaces between chains.
- B–C · 637 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 366 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 5E2H · Crystal Structure of D-alanine Carboxypeptidase AmpC from Mycobacterium smegmatis · 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 A0QZC8
- Elsewhere: RCSB PDB 5E2H · PDBe 5E2H · UniProt A0QZC8
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