Research workbench
Crystal structure of penicillin binding protein 4 (dacb) from haemophilus influenzae, complexed with novel beta-lactam (CMV)
Analyse Crystal structure of penicillin binding protein 4 (dacb) from haemophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A3E
- Type
- protein
- Length
- 871 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 4
- EC
- 3.4.16.4
- UniProt
- A8E0K8
- Ligands
- CMV
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 4 (EC 3.4.16.4) | protein | 438 | 31% helix, 26% strand | A8E0K8 |
| B | Penicillin-binding protein 4 (EC 3.4.16.4) | protein | 433 | 31% helix, 28% strand | A8E0K8 |
Ligands and binding sites
- CMV · (2R,4S)-2-[(1R)-1-({(2R)-2-[(4-ethyl-2,3-dioxopiperazin-1-yl)amino]-2-phenylacetyl}amino)-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.80 | 0.92 | 54 | empty |
| 2 | 512 | 0.65 | 0.77 | 62 | empty |
| 3 | 438 | 0.65 | 0.78 | 45 | empty |
| 4 | 139 | 0.49 | 0.78 | 26 | empty |
| 5 | 141 | 0.46 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1633 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3A3E · Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae… · 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 A8E0K8
- Elsewhere: RCSB PDB 3A3E · PDBe 3A3E · UniProt A8E0K8
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