MolNFT v1 · #103548 · protein
Crystal structure of T4 lysozyme-peptide in complex with teicoplanin- A2-2
4PK0 · Teicoplanin-A2-2: “Crystal structure of T4 lysozyme-peptide in complex with teicoplanin- A2-2”. X-ray diffraction, 7 ligands (T55, GCS, NAG), 2 pockets (best druggability 0.57). MolNFT v1 #103548 on GenesisL1: 3D structure, binding…
- PDB
- 4PK0
- Type
- protein
- Length
- 178 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Teicoplanin-A2-2; Lysozyme
- EC
- 3.2.1.17
- UniProt
- D9IEF7
- Ligands
- T55, GCS, NAG, MAN, NA, CL, PO4
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Teicoplanin-A2-2 | protein | 7 | 0% helix, 29% strand | — |
| A | Lysozyme (EC 3.2.1.17) | protein | 171 | 62% helix, 10% strand | D9IEF7 |
Ligands and binding sites
- T55 · 8-methylnonanoic acid · ligand · chains B, A
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B, A
- MAN · alpha-D-mannopyranose · sugar · chains B, A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains B, A
- GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.57 | 0.75 | 37 | empty |
| 2 | 58 | 0.32 | 0.76 | 13 | T55 |
Interfaces
1 interface between chains.
- B–A · 579 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 3 d-amino, 3 glycan (nonstandard, D-amino acid, glycosylation, methylation).
Compared structures
- 4PK0 · Crystal structure of T4 lysozyme-peptide in complex with teicoplanin-A2-2 · the same entry in another collection · chain B against B, 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 D9IEF7
- Elsewhere: RCSB PDB 4PK0 · PDBe 4PK0 · UniProt D9IEF7
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