Research workbench
Crystal structure of penicillin binding protein 4 (dacb) from haemophilus influenzae
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
- 3A3D
- 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
- 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
- GOL · Glycerol · additive · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.84 | 0.85 | 101 | GOL |
| 2 | 424 | 0.81 | 0.89 | 75 | empty |
| 3 | 95 | 0.53 | 0.84 | 17 | empty |
| 4 | 72 | 0.52 | 0.86 | 16 | empty |
| 5 | 76 | 0.42 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2283 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3A3D · 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 3A3D · PDBe 3A3D · UniProt A8E0K8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.