MolNFT v1 · #156473 · protein

Human serum albumin with cyclic peptide dalbavancin

6M5E: “Human serum albumin with cyclic peptide dalbavancin”. X-ray diffraction, 7 ligands (JEF, DIB, M12), 20 pockets (best druggability 0.85). MolNFT v1 #156473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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.

Pocket	Volume (Å³)	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 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 525 Å² buried · 7 hydrogen bonds · protein-protein
C–H · 351 Å² buried · 5 hydrogen bonds · protein-protein
B–G · 349 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 347 Å² 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

6M5E · Human serum albumin with cyclic peptide dalbavancin · the same entry in another collection · chain J against J, TM-score 1.00
P02768 · AlphaFold monomer V2.0 prediction for albumin (P02768) · a predicted model of the same protein · chain B against A, TM-score 0.97

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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