MolNFT v1 · #27616 · protein
Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from streptococcus pneumoniae
1XP4 · D-alanyl-D-alanine carboxypeptidase: “Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from streptococcus pneumoniae”. X-ray diffraction, 2 ligands (IOD, SO4), 15 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 1XP4
- Type
- protein
- Length
- 1,388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- Q8DQ99
- Ligands
- IOD, SO4
- Pockets
- 15 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 369 | 27% helix, 27% strand | Q8DQ99 |
| B | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 339 | 28% helix, 23% strand | Q8DQ99 |
| C | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 359 | 29% helix, 26% strand | Q8DQ99 |
| D | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 321 | 30% helix, 25% strand | Q8DQ99 |
Ligands and binding sites
- IOD · Iodide ion · ion · 16 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.64 | 0.81 | 30 | empty |
| 2 | 255 | 0.62 | 0.81 | 31 | empty |
| 3 | 380 | 0.59 | 0.75 | 34 | empty |
| 4 | 165 | 0.47 | 0.76 | 26 | IOD |
| 5 | 176 | 0.47 | 0.76 | 32 | SO4, IOD |
Interfaces
3 interfaces between chains.
- A–D · 846 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 251 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 200 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 1XP4 · Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from… · 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 Q8DQ99
- Elsewhere: RCSB PDB 1XP4 · PDBe 1XP4 · UniProt Q8DQ99
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