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Structural coordination of polymerization and crosslinking by a peptidoglycan synthase complex
Analyse Structural coordination of polymerization and crosslinking by a peptidoglycan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PL6
- Type
- protein
- Length
- 924 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan glycosyltransferase roda; Penicillin-binding protein 2/CELL division…
- EC
- 2.4.1.129
- UniProt
- Q5SIX3, Q5SJ23
- Ligands
- AIX
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan glycosyltransferase roda (EC 2.4.1.129) | protein | 336 | 71% helix, 1% strand | Q5SIX3 |
| B | Penicillin-binding protein 2/CELL division protein ftsi | protein | 577 | 34% helix, 18% strand | Q5SJ23 |
| D | Unknown peptide | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- AIX · (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.78 | 0.80 | 132 | empty |
| 2 | 54 | 0.63 | 0.93 | 20 | empty |
| 3 | 266 | 0.62 | 0.80 | 41 | AIX |
| 4 | 250 | 0.52 | 0.75 | 24 | empty |
| 5 | 136 | 0.51 | 0.79 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1716 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 383 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6PL6 · Structural coordination of polymerization and crosslinking by a peptidoglycan synthase… · 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 Q5SIX3
- Every structure of UniProt Q5SJ23
- Elsewhere: RCSB PDB 6PL6 · PDBe 6PL6 · UniProt Q5SIX3 · UniProt Q5SJ23
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