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A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct
Analyse A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LQB
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- L,D-transpeptidase 2
- EC
- 2.3.2.-
- UniProt
- I6Y9J2
- Ligands
- 2RG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.7 · 2 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 267 | 12% helix, 39% strand | I6Y9J2 |
| B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 264 | 13% helix, 39% strand | I6Y9J2 |
Ligands and binding sites
- 2RG · (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl) carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACY · Acetic acid · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.71 | 0.76 | 83 | 2RG |
| 2 | 86 | 0.47 | 0.82 | 21 | ACY |
| 3 | 168 | 0.46 | 0.75 | 30 | 2RG |
| 4 | 79 | 0.41 | 0.79 | 20 | empty |
| 5 | 61 | 0.34 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 414 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6LQB · A third intermediate state of L,D-transpeptidase LDTMT2-ertapenem adduct · 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 A against A, TM-score 0.96
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 6LQB · PDBe 6LQB · UniProt I6Y9J2
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