Research workbench
Michaelis complex of streptomyces R61 dd-peptidase with a specific peptidoglycan substrate fragment
Analyse Michaelis complex of streptomyces R61 dd-peptidase with a specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IKG
- Type
- protein
- Length
- 345 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- P15555
- Ligands
- REX
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 345 | 35% helix, 21% strand | P15555 |
Ligands and binding sites
- REX · Glycyl-L-alpha-amino-epsilon-pimelyl-D-alanyl-D-alanine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.56 | 0.77 | 35 | REX |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1IKG · Michaelis complex of streptomyces R61 dd-peptidase with a specific peptidoglycan… · the same entry in another collection · chain A against A, TM-score 1.00
- P15555 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase (P15555) · a predicted model of the same protein · 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 P15555
- Elsewhere: RCSB PDB 1IKG · PDBe 1IKG · UniProt P15555
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