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Crystal structure of hsa soaked with cisplatin for one week

Analyse Crystal structure of hsa soaked with cisplatin for one week in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WOK
Type: protein
Length: 1,118 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Albumin
UniProt: P02768
Ligands: CPT, PO4
Pockets: 17 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Albumin	protein	559	70% helix, 0% strand	P02768
B	Albumin	protein	559	72% helix, 0% strand	P02768

Ligands and binding sites

CPT · Cisplatin · ligand · 10 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1121	0.86	0.87	116	empty
2	560	0.84	0.89	70	empty
3	554	0.79	0.85	55	PO4
4	96	0.71	0.93	21	empty
5	240	0.68	0.84	38	empty

Interfaces

1 interface between chains.

A–B · 741 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide (disulfide).

Compared structures

7WOK · Crystal structure of HSA soaked with cisplatin for one week · 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 0.98

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 7WOK · PDBe 7WOK · UniProt P02768

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