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Crystal structure of human serum albumin complex with jms-053

Analyse Crystal structure of human serum albumin complex with jms-053 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WUW
Type: protein
Length: 1,164 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serum albumin
UniProt: P02768
Ligands: MYR, UAY, UNL, OCA
Pockets: 15 · best druggability 0.90

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Serum albumin	protein	582	74% helix, 0% strand	P02768

Ligands and binding sites

MYR · Myristic acid · ligand · 9 copies · chains A, B
UAY · 7-imino-2-phenylthieno[3,2-c]pyridine-4,6(5H,7H)-dione · ligand · 2 copies · chains A, B
UNL · Unknown ligand · ligand · 2 copies · chains A, B
OCA · Octanoic acid (caprylic acid) · ligand · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B

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

Pockets

15 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	1125	0.90	0.92	121	EDO, MYR, PG4
2	961	0.89	0.91	99	MYR, PG4, OCA, EDO
3	422	0.80	0.88	52	MYR
4	331	0.76	0.86	34	UAY, UNL
5	381	0.75	0.85	36	UAY, UNL

Interfaces

1 interface between chains.

A–B · 914 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide (disulfide).

Compared structures

6WUW · Crystal structure of Human Serum Albumin complex with JMS-053 · 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 B against A, TM-score 0.86

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 6WUW · PDBe 6WUW · UniProt P02768

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