Research workbench
Crystal structure of penicillin binding protein 4 (dacb) from haemophilus influenzae, complexed with ampicillin (aix)
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
- 3A3I
- Type
- protein
- Length
- 906 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
- AIX
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Penicillin-binding protein 4 (EC 3.4.16.4) | protein | 453 | 32% helix, 26% strand | A8E0K8 |
Ligands and binding sites
- AIX · (2R,4S)-2-[(1R)-1-{[(2R)-2-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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.84 | 0.85 | 93 | empty |
| 2 | 264 | 0.81 | 0.93 | 51 | empty |
| 3 | 217 | 0.60 | 0.80 | 31 | AIX |
| 4 | 85 | 0.50 | 0.83 | 17 | empty |
| 5 | 77 | 0.45 | 0.81 | 15 | AIX |
Interfaces
1 interface between chains.
- A–B · 2251 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3A3I · 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 3A3I · PDBe 3A3I · UniProt A8E0K8
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