MolNFT v1 · #189326 · protein

Cryo-EM structure of human ntcp complexed with YN69202FAB

7VAD · SODIUM/BILE acid cotransporter: “Cryo-EM structure of human ntcp complexed with YN69202FAB”. Electron microscopy, 11 pockets (best druggability 0.71). MolNFT v1 #189326 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VAD
Type: protein
Length: 743 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SODIUM/BILE acid cotransporter; Fab heavy chain from antibody IgG clone number YN69202…
UniProt: Q14973
Pockets: 11 · best druggability 0.71

Structure

electron microscopy · 3 distinct chains · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SODIUM/BILE acid cotransporter	protein	306	76% helix, 0% strand	Q14973
H	Fab heavy chain from antibody IgG clone number YN69202	protein	221	3% helix, 45% strand	—
L	Fab light chain from antibody IgG clone number YN69202	protein	216	2% helix, 40% strand	—

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	802	0.71	0.76	57	empty
2	246	0.58	0.79	40	empty
3	172	0.56	0.80	26	empty
4	312	0.56	0.76	35	empty
5	133	0.51	0.79	13	empty

Interfaces

3 interfaces between chains.

H–L · 1786 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 782 Å² buried · 14 hydrogen bonds · protein-protein
A–L · 446 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7VAD · Cryo-EM structure of human NTCP complexed with YN69202Fab · the same entry in another collection · chain A against A, TM-score 1.00
Q14973 · AlphaFold monomer V2.0 prediction for SODIUM/BILE acid cotransporter (Q14973) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 Q14973
Elsewhere: RCSB PDB 7VAD · PDBe 7VAD · UniProt Q14973

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