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Crystal structure of NB.B201 bound to human serum albumin

Analyse Crystal structure of NB.B201 bound to human serum albumin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VNW
Type: protein
Length: 1,404 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serum albumin; NB.B201
UniProt: P02768
Ligands: PLM, DAO, BUA
Pockets: 19 · best druggability 0.90

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serum albumin	protein	583	72% helix, 0% strand	P02768
B	Serum albumin	protein	581	72% helix, 0% strand	P02768
C, D	NB.B201	protein	120	3% helix, 55% strand	—

Ligands and binding sites

PLM · Palmitic acid · ligand · 2 copies · chains A, B
DAO · Lauric acid · ligand · chains A
BUA · butanoic acid · ligand · chains B
GOL · Glycerol · additive · 4 copies · chains A, C

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

Pockets

19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.90	0.91	119	PLM, DAO
2	1127	0.90	0.91	121	PLM, BUA
3	457	0.76	0.84	42	empty
4	55	0.69	0.96	16	empty
5	331	0.67	0.81	23	GOL

Interfaces

4 interfaces between chains.

A–D · 529 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 492 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 334 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 36 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 36 disulfide (disulfide).

Compared structures

5VNW · Crystal structure of Nb.b201 bound to human serum albumin · 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 0.84

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 5VNW · PDBe 5VNW · UniProt P02768

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