MolNFT v1 · #54052 · protein
Structural insights into the catalytic mechanism and the role of streptococcus pneumoniae PBP1B
2XD5 · Penicillin-binding protein 1B: “Structural insights into the catalytic mechanism and the role of streptococcus pneumoniae PBP1B”. X-ray diffraction, 3 ligands (S2D, SO4, CL), 10 pockets (best druggability 0.70). MolNFT v1 #54052 on…
- PDB
- 2XD5
- Type
- protein
- Length
- 937 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B
- EC
- 2.3.2.-, 2.4.1.129
- UniProt
- Q7CRA4
- Ligands
- S2D, SO4, CL
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.3.2.-, 2.4.1.129) | protein | 469 | 38% helix, 20% strand | Q7CRA4 |
| B | Penicillin-binding protein 1B (EC 2.3.2.-, 2.4.1.129) | protein | 468 | 35% helix, 21% strand | Q7CRA4 |
Ligands and binding sites
- S2D · N-benzoyl-D-alanine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.70 | 0.77 | 81 | S2D, CL |
| 2 | 168 | 0.46 | 0.76 | 29 | SO4 |
| 3 | 131 | 0.42 | 0.75 | 28 | SO4 |
| 4 | 124 | 0.39 | 0.75 | 18 | empty |
| 5 | 126 | 0.39 | 0.74 | 15 | CL |
Interfaces
1 interface between chains.
- A–B · 569 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2XD5 · Structural insights into the catalytic mechanism and the role of Streptococcus pneumoniae… · 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 2XD5 · PDBe 2XD5 · UniProt Q7CRA4
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