MolNFT v2 · #159536 · protein
Crystal structure of E. coli PBP5-meropenem
6NTZ · D-alanyl-D-alanine carboxypeptidase: “Crystal structure of E. coli PBP5-meropenem”. X-ray diffraction at 2.2, 1 ligand (MXR), 2 pockets (best druggability 0.42). MolNFT v2 #159536 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NTZ
- Type
- protein
- Length
- 367 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Escherichia coli
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- A0A0A0GRC5
- Ligands
- MXR
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 367 | 31% helix, 31% strand | A0A0A0GRC5 |
Ligands and binding sites
- MXR · (2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.42 | 0.75 | 27 | MXR |
| 2 | 98 | 0.37 | 0.75 | 24 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6NTZ · Crystal structure of E. COLI PBP5-meropenem · 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 A0A0A0GRC5
- Elsewhere: RCSB PDB 6NTZ · PDBe 6NTZ · UniProt A0A0A0GRC5
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