Research workbench

Cryoem structure of kdelr with legobody

Analyse Cryoem structure of kdelr with legobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RXC
Type: protein
Length: 1,178 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAB_8D3_2 heavy chain; FAB_8D3_2 light chain; NB_KR; Maltodextrin-binding…
UniProt: A0A4Z0THX4, P99134, P06654, Q5ZKX9
Ligands: POV, GLC
Pockets: 11 · best druggability 0.78

Structure

electron microscopy · 5 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	FAB_8D3_2 heavy chain	protein	207	4% helix, 51% strand	—
L	FAB_8D3_2 light chain	protein	204	7% helix, 52% strand	—
N	NB_KR	protein	126	2% helix, 52% strand	—
B	Maltodextrin-binding PROTEIN,IMMUNOGLOBULIN G-binding protein A,IMMUNOGLOBULIN G-binding protein G	protein	439	46% helix, 19% strand	A0A4Z0THX4, P99134, P06654
K	Er lumen protein-retaining receptor 2	protein	202	76% helix, 0% strand	Q5ZKX9

Ligands and binding sites

POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 4 copies · chains K
GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	149	0.78	0.95	24	empty
2	308	0.75	0.87	28	GLC
3	200	0.63	0.84	39	empty
4	593	0.61	0.74	66	empty
5	58	0.57	0.90	18	empty

Interfaces

7 interfaces between chains.

H–L · 1710 Å² buried · 17 hydrogen bonds · protein-protein
N–K · 1254 Å² buried · 12 hydrogen bonds · protein-protein
H–B · 654 Å² buried · 12 hydrogen bonds · protein-protein
N–B · 611 Å² buried · 9 hydrogen bonds · protein-protein
L–N · 589 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7RXC · CryoEM structure of KDELR with Legobody · the same entry in another collection · chain K against K, TM-score 1.00
Q5ZKX9 · AlphaFold monomer V2.0 prediction for er lumen protein-retaining receptor 2 (Q5ZKX9) · a predicted model of the same protein · chain K against A, TM-score 0.93
P06654 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P06654) · a predicted model of the same protein · chain B against A, TM-score 0.18
P99134 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P99134) · a predicted model of the same protein · chain B against A, TM-score 0.18

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 A0A4Z0THX4
Every structure of UniProt P99134
Every structure of UniProt P06654
Every structure of UniProt Q5ZKX9
Elsewhere: RCSB PDB 7RXC · PDBe 7RXC · UniProt A0A4Z0THX4 · UniProt P99134 · UniProt P06654 · UniProt Q5ZKX9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.