MolNFT v1 · #185139 · protein

NAV_AE1/SP1CTD_PORE-ANT05 complex

7PG8 · ANT05 H12 Fab fragment, light chain: “NAV_AE1/SP1CTD_PORE-ANT05 complex”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #185139 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7PG8
Type: protein
Length: 4,517 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ANT05 H12 Fab fragment, light chain; ANT05 H12 Fab fragment, heavy chain; Ion transport…
UniProt: Q0ABW0, F7IVA8
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P, M, V, S, G, D, J, A	ANT05 H12 Fab fragment, light chain	protein	215	5% helix, 47% strand	—
B, F, I, L, N, R, U, X	ANT05 H12 Fab fragment, heavy chain	protein	221	6% helix, 39% strand	—
C	Ion transport PROTEIN,VOLTAGE-gated sodium channel	protein	127	84% helix, 0% strand	Q0ABW0, F7IVA8
E	Ion transport PROTEIN,VOLTAGE-gated sodium channel	protein	128	83% helix, 0% strand	Q0ABW0, F7IVA8
H, O, T	Ion transport PROTEIN,VOLTAGE-gated sodium channel	protein	130	80% helix, 0% strand	Q0ABW0, F7IVA8
K, W	Ion transport PROTEIN,VOLTAGE-gated sodium channel	protein	129	84% helix, 0% strand	Q0ABW0, F7IVA8
Q	Ion transport PROTEIN,VOLTAGE-gated sodium channel	protein	126	80% helix, 0% strand	Q0ABW0, F7IVA8

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1099	0.79	0.81	123	empty
2	638	0.79	0.85	98	empty
3	1033	0.79	0.81	144	empty
4	680	0.79	0.84	93	empty
5	610	0.79	0.85	91	empty

Interfaces

26 interfaces between chains.

A–B · 631 Å² buried · 0 hydrogen bonds · protein-protein
M–N · 613 Å² buried · 0 hydrogen bonds · protein-protein
P–R · 613 Å² buried · 0 hydrogen bonds · protein-protein
V–X · 610 Å² buried · 0 hydrogen bonds · protein-protein
J–L · 606 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7PG8 · NaV_Ae1/Sp1CTD_pore-ANT05 complex · the same entry in another collection · chain P against P, TM-score 1.00

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 Q0ABW0
Every structure of UniProt F7IVA8
Elsewhere: RCSB PDB 7PG8 · PDBe 7PG8 · UniProt Q0ABW0 · UniProt F7IVA8

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