MolNFT v1 · #164461 · protein
Crystal structure of Y. pestis penicillin-binding protein 3
6SYN · Peptidoglycan D,D-transpeptidase ftsi: “Crystal structure of Y. pestis penicillin-binding protein 3”. X-ray diffraction, 1 ligand (CB9), 4 pockets (best druggability 0.59). MolNFT v1 #164461 on GenesisL1: 3D structure, binding sites…
- PDB
- 6SYN
- Type
- protein
- Length
- 471 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan D,D-transpeptidase ftsi
- EC
- 3.4.16.4
- UniProt
- Q0WJB8
- Ligands
- CB9
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 471 | 34% helix, 23% strand | Q0WJB8 |
Ligands and binding sites
- CB9 · (2R,4S)-2-[(1R)-1-{[(2S)-2-carboxy-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.59 | 0.79 | 36 | ACT, CB9 |
| 2 | 100 | 0.53 | 0.83 | 25 | empty |
| 3 | 52 | 0.32 | 0.77 | 14 | empty |
| 4 | 51 | 0.28 | 0.74 | 10 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6SYN · Crystal structure of Y. pestis penicillin-binding protein 3 · 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 Q0WJB8
- Elsewhere: RCSB PDB 6SYN · PDBe 6SYN · UniProt Q0WJB8
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