MolNFT v1 · #104989 · protein
Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis and antibiotic resistance: calcium binding promotes dimer formation
4QRA · L,D-transpeptidase ldtb: “Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis and antibiotic resistance…”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.68). MolNFT v1 #104989 on…
- PDB
- 4QRA
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase ldtb
- UniProt
- I6Y9J2
- Ligands
- CA
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase ldtb | protein | 334 | 10% helix, 37% strand | I6Y9J2 |
| B | L,D-transpeptidase ldtb | protein | 330 | 10% helix, 37% strand | I6Y9J2 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.68 | 0.78 | 43 | empty |
| 2 | 631 | 0.68 | 0.77 | 65 | empty |
| 3 | 161 | 0.48 | 0.77 | 27 | empty |
| 4 | 146 | 0.47 | 0.77 | 27 | empty |
| 5 | 152 | 0.42 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 783 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4QRA · Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and… · the same entry in another collection · chain A against A, TM-score 1.00
- I6Y9J2 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (I6Y9J2) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 I6Y9J2
- Elsewhere: RCSB PDB 4QRA · PDBe 4QRA · UniProt I6Y9J2
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