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Cryo-EM structure of rat ntcp complexed with YN69202FAB

Analyse Cryo-EM structure of rat ntcp complexed with YN69202FAB in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VAF
Type: protein
Length: 734 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain from antibody IgG clone number YN69202; Fab light chain from antibody IgG…
UniProt: P26435
Pockets: 9 · best druggability 0.74

Structure

electron microscopy · 3 distinct chains · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain from antibody IgG clone number YN69202	protein	221	1% helix, 49% strand	—
L	Fab light chain from antibody IgG clone number YN69202	protein	216	6% helix, 42% strand	—
A	SODIUM/BILE acid cotransporter	protein	297	75% helix, 0% strand	P26435

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1014	0.74	0.76	72	empty
2	365	0.57	0.75	48	empty
3	229	0.52	0.76	37	empty
4	137	0.45	0.77	24	empty
5	59	0.42	0.82	14	empty

Interfaces

3 interfaces between chains.

H–L · 1784 Å² buried · 10 hydrogen bonds · protein-protein
H–A · 596 Å² buried · 7 hydrogen bonds · protein-protein
L–A · 353 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7VAF · Cryo-EM structure of Rat NTCP complexed with YN69202Fab · the same entry in another collection · chain H against H, TM-score 1.00
P26435 · AlphaFold monomer V2.0 prediction for SODIUM/BILE acid cotransporter (P26435) · a predicted model of the same protein · chain A against A, TM-score 0.77

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 P26435
Elsewhere: RCSB PDB 7VAF · PDBe 7VAF · UniProt P26435

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