MolNFT v1 · #102819 · protein
Structure of the ldcb ld-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
4OXD: “Structure of the ldcb ld-carboxypeptidase reveals the molecular basis of peptidoglycan recognition”. X-ray diffraction, 6 ligands (MUB, DSG, LYS), 13 pockets (best druggability 0.74). MolNFT v1 #102819 on GenesisL1: 3D structure…
- PDB
- 4OXD
- Type
- protein
- Length
- 878 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ldcb ld-carboxypeptidase; Mub-ala-zgl-lys-dsg
- UniProt
- Q8DQQ1
- Ligands
- MUB, DSG, LYS, ZN, MG, CL
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ldcb ld-carboxypeptidase | protein | 185 | 37% helix, 14% strand | Q8DQQ1 |
| B | Ldcb ld-carboxypeptidase | protein | 181 | 39% helix, 13% strand | Q8DQQ1 |
| C | Ldcb ld-carboxypeptidase | protein | 167 | 37% helix, 17% strand | Q8DQQ1 |
| D | Ldcb ld-carboxypeptidase | protein | 171 | 36% helix, 17% strand | Q8DQQ1 |
| E | Ldcb ld-carboxypeptidase | protein | 171 | 33% helix, 13% strand | Q8DQQ1 |
| H | Mub-ala-zgl-lys-dsg | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- MUB · N-acetyl-alpha-muramic acid · ligand · chains A, C, H
- DSG · D-asparagine · ligand · chains A, H
- LYS · Lysine · ligand · chains B
- ZN · Zinc ion · metal · 18 copies · chains A, H, B, E, C, D
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.74 | 0.80 | 66 | MUB |
| 2 | 690 | 0.74 | 0.80 | 56 | empty |
| 3 | 733 | 0.70 | 0.77 | 75 | empty |
| 4 | 89 | 0.54 | 0.85 | 20 | empty |
| 5 | 58 | 0.51 | 0.87 | 16 | empty |
Interfaces
9 interfaces between chains.
- A–B · 515 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 350 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 223 Ų buried · 1 hydrogen bond · protein-protein
- B–E · 213 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 4OXD · 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 4OXD · PDBe 4OXD · UniProt Q8DQQ1
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