MolNFT v1 · #158440 · protein
Crystal structure of E. COLI ycbb
6NTW · Probable L,D-transpeptidase ycbb: “Crystal structure of E. COLI ycbb”. X-ray diffraction, 2 ligands (MXR, SO4), 5 pockets (best druggability 0.60). MolNFT v1 #158440 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NTW
- Type
- protein
- Length
- 505 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable L,D-transpeptidase ycbb
- EC
- 2.-.-.-
- UniProt
- P22525
- Ligands
- MXR, SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable L,D-transpeptidase ycbb (EC 2.-.-.-) | protein | 505 | 42% helix, 14% strand | P22525 |
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
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.60 | 0.77 | 50 | empty |
| 2 | 251 | 0.56 | 0.77 | 30 | MXR |
| 3 | 86 | 0.49 | 0.82 | 18 | empty |
| 4 | 120 | 0.38 | 0.74 | 25 | empty |
| 5 | 53 | 0.32 | 0.77 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 P22525
- Elsewhere: RCSB PDB 6NTW · PDBe 6NTW · UniProt P22525
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