Research workbench

Cryo-EM structure of the ir subunit from X. laevis npc

Analyse Cryo-EM structure of the ir subunit from X. laevis npc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WKK
Type: protein
Length: 18,728 residues
Chains: 30
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MGC83295 protein; NUP188 domain-containing protein; Nuclear pore complex protein NUP93…
UniProt: Q642R6, A0A1L8F1N1, Q7ZX96, Q7ZWL0, K9ZTJ6, Q91349, Q5EAX5, Q6DCM0, Q6AX31
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 18 distinct chains · 63% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MGC83295 protein	protein	1684	73% helix, 1% strand	Q642R6
B, b	NUP188 domain-containing protein	protein	1482	74% helix, 2% strand	A0A1L8F1N1
C, c	Nuclear pore complex protein NUP93	protein	633	74% helix, 2% strand	Q7ZX96
D	NUP155-prov protein	protein	1115	51% helix, 18% strand	Q7ZWL0
E, e	Nuclear pore complex protein NUP93	protein	625	74% helix, 2% strand	Q7ZX96
F	NUP155-prov protein	protein	1094	53% helix, 17% strand	Q7ZWL0
G, g	NUP54	protein	215	73% helix, 5% strand	K9ZTJ6
H, h	IL4I1 protein	protein	163	90% helix, 0% strand	Q91349
I, i	MGC84997 protein	protein	171	90% helix, 0% strand	Q5EAX5
J, j	NUP54	protein	195	72% helix, 3% strand	K9ZTJ6
L, l	IL4I1 protein	protein	156	96% helix, 0% strand	Q91349
K, k	MGC84997 protein	protein	166	89% helix, 0% strand	Q5EAX5
M, m	NUP155-prov protein	protein	869	40% helix, 22% strand	Q7ZWL0
a	MGC83295 protein	protein	1669	73% helix, 1% strand	Q642R6
d	NUP155-prov protein	protein	1123	52% helix, 16% strand	Q7ZWL0
f	NUP155-prov protein	protein	1097	54% helix, 17% strand	Q7ZWL0
O, o	Aaas-prov protein	protein	367	3% helix, 43% strand	Q6DCM0
N, n	Nucleoporin NDC1	protein	431	76% helix, 1% strand	Q6AX31

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	1242	0.86	0.87	173	empty
2	1518	0.84	0.85	169	empty
3	1002	0.83	0.84	124	empty
4	2021	0.83	0.84	232	empty
5	1555	0.82	0.83	178	empty

Interfaces

54 interfaces between chains.

j–l · 1549 Å² buried · 0 hydrogen bonds · protein-protein
G–I · 1419 Å² buried · 0 hydrogen bonds · protein-protein
J–L · 1406 Å² buried · 1 hydrogen bond · protein-protein
J–K · 1160 Å² buried · 0 hydrogen bonds · protein-protein
j–k · 1129 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7WKK · Cryo-EM structure of the IR subunit from X. laevis NPC · the same entry in another collection · chain J against J, 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 Q642R6
Every structure of UniProt A0A1L8F1N1
Every structure of UniProt Q7ZX96
Every structure of UniProt Q7ZWL0
Every structure of UniProt K9ZTJ6
Every structure of UniProt Q91349
Every structure of UniProt Q5EAX5
Every structure of UniProt Q6DCM0
Every structure of UniProt Q6AX31
Elsewhere: RCSB PDB 7WKK · PDBe 7WKK · UniProt Q642R6 · UniProt A0A1L8F1N1 · UniProt Q7ZX96 · UniProt Q7ZWL0 · UniProt K9ZTJ6 · UniProt Q91349 · UniProt Q5EAX5 · UniProt Q6DCM0 · UniProt Q6AX31

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