MolNFT v1 · #102812 · protein
Structure of the ldcb ld-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
4OX5: “Structure of the ldcb ld-carboxypeptidase reveals the molecular basis of peptidoglycan recognition”. X-ray diffraction, 3 ligands (DAL, ZN, CL), 2 pockets (best druggability 0.52). MolNFT v1 #102812 on GenesisL1: 3D structure…
- PDB
- 4OX5
- Type
- protein
- Length
- 184 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ldcb ld-carboxypeptidase
- UniProt
- Q8DQQ1
- Ligands
- DAL, ZN, CL
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ldcb ld-carboxypeptidase | protein | 184 | 39% helix, 16% strand | Q8DQQ1 |
Ligands and binding sites
- DAL · D-alanine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.52 | 0.82 | 20 | DAL |
| 2 | 51 | 0.50 | 0.87 | 16 | empty |
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 4OX5 · Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan… · 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 Q8DQQ1
- Elsewhere: RCSB PDB 4OX5 · PDBe 4OX5 · UniProt Q8DQQ1
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