Research workbench

Human serum albumin-palmitic acid-FE(HN3PIT)CL2

Analyse Human serum albumin-palmitic acid-FE(HN3PIT)CL2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GIX
Type: protein
Length: 1,162 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serum albumin
UniProt: P02768
Ligands: PLM, 6WF
Pockets: 11 · best druggability 0.91

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Serum albumin	protein	581	74% helix, 0% strand	P02768

Ligands and binding sites

PLM · Palmitic acid · ligand · 12 copies · chains A, B
6WF · 14-piperidin-1-yl-11-oxa-13$l^{3}-thia-15,16$l^{4}-diaza-12$l^{3}-ferratetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),2(7),3,5,8,13,16-heptaene · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1111	0.91	0.93	122	6WF, PLM
2	1095	0.89	0.90	117	6WF, PLM
3	933	0.77	0.79	88	PLM
4	669	0.76	0.82	59	PLM
5	339	0.73	0.85	36	PLM

Interfaces

1 interface between chains.

A–B · 251 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide, 3 lipid, 1 covalent (disulfide, palmitoylation, covalent ligand).

Compared structures

5GIX · Human serum albumin-Palmitic acid-Fe(Hn3piT)Cl2 · the same entry in another collection · chain A against A, TM-score 1.00
P02768 · AlphaFold monomer V2.0 prediction for albumin (P02768) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 5GIX · PDBe 5GIX · UniProt P02768

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