MolNFT v1 · #144747 · protein
Apo crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4)
6C39 · Serine-type D-ala-D-ala carboxypeptidase: “Apo crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4)”. X-ray diffraction, 3 ligands (ZN, NA, SO4), 5 pockets (best druggability 0.76). MolNFT v1 #144747 on…
- PDB
- 6C39
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine-type D-ala-D-ala carboxypeptidase
- UniProt
- A0A133Q5K3
- Ligands
- ZN, NA, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine-type D-ala-D-ala carboxypeptidase | protein | 359 | 33% helix, 26% strand | A0A133Q5K3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.76 | 0.87 | 39 | empty |
| 2 | 183 | 0.55 | 0.80 | 27 | SO4 |
| 3 | 163 | 0.53 | 0.80 | 27 | SO4 |
| 4 | 190 | 0.45 | 0.74 | 30 | empty |
| 5 | 60 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 547 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6C39 · Apo crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) · 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 A0A133Q5K3
- Elsewhere: RCSB PDB 6C39 · PDBe 6C39 · UniProt A0A133Q5K3
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