Research workbench
Human serum albumin with cyclic peptide dalbavancin
Analyse Human serum albumin with cyclic peptide dalbavancin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M5E
- Type
- protein
- Length
- 1,778 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin; Dalbavancin
- UniProt
- P02768
- Ligands
- JEF, DIB, M12, F8F, F8X, WOO, MAN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Serum albumin | protein | 581 | 72% helix, 0% strand | P02768 |
| F, G, H, I, J | Dalbavancin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- JEF · O-(O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500) · ligand · 6 copies · chains A, B, C
- DIB · 3-amino-(dimethylpropylamine) · ligand · 5 copies · chains A, F, B, G, C, H, I, J
- M12 · 10-methylundecanoic acid · ligand · 5 copies · chains A, F, B, G, C, H, I, J
- F8F · (2S,5S)-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid · ligand · 3 copies · chains A, F, B, G, C, H
- F8X · 2-amino-2-deoxy-beta-D-altropyranuronic acid · ligand · 2 copies · chains C, I, B, J
- WOO · beta-L-allopyranose · ligand · 2 copies · chains B, I, J
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.85 | 0.87 | 92 | JEF |
| 2 | 699 | 0.84 | 0.87 | 78 | JEF |
| 3 | 508 | 0.83 | 0.89 | 64 | JEF |
| 4 | 106 | 0.75 | 0.95 | 24 | empty |
| 5 | 383 | 0.75 | 0.85 | 40 | empty |
Interfaces
9 interfaces between chains.
- A–B · 734 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 525 Ų buried · 7 hydrogen bonds · protein-protein
- C–H · 351 Ų buried · 5 hydrogen bonds · protein-protein
- B–G · 349 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 347 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 30 modified, 12 covalent, 3 glycan (disulfide, nonstandard, covalent ligand, glycosylation).
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 P02768
- Elsewhere: RCSB PDB 6M5E · PDBe 6M5E · UniProt P02768
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