MolNFT v1 · #54048 · protein
Active site restructuring regulates ligand recognition in class a penicillin-binding proteins
2XD1 · Penicillin-binding protein 1B: “Active site restructuring regulates ligand recognition in class a penicillin-binding proteins”. X-ray diffraction, 2 ligands (CEF, SO4), 12 pockets (best druggability 0.59). MolNFT v1 #54048 on…
- PDB
- 2XD1
- Type
- protein
- Length
- 924 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B
- EC
- 2.4.1.129, 2.3.2.-
- UniProt
- Q7CRA4
- Ligands
- CEF, SO4
- Pockets
- 12 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.4.1.129, 2.3.2.-) | protein | 469 | 38% helix, 21% strand | Q7CRA4 |
| B | Penicillin-binding protein 1B (EC 2.4.1.129, 2.3.2.-) | protein | 455 | 37% helix, 20% strand | Q7CRA4 |
Ligands and binding sites
- CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.59 | 0.76 | 38 | CEF |
| 2 | 363 | 0.58 | 0.76 | 38 | CEF |
| 3 | 181 | 0.46 | 0.75 | 30 | SO4 |
| 4 | 156 | 0.45 | 0.76 | 25 | SO4 |
| 5 | 124 | 0.40 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2XD1 · Active site restructuring regulates ligand recognition in class a penicillin-binding… · 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 Q7CRA4
- Elsewhere: RCSB PDB 2XD1 · PDBe 2XD1 · UniProt Q7CRA4
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