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Protein peptide complex

Analyse Protein peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QXP
Type: protein
Length: 3,066 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucine-rich repeat extensin-like protein 2; Protein ralf-like 4
UniProt: O48809, Q9FZA0
Ligands: NAG, BMA, MAN
Pockets: 16 · best druggability 0.59

Structure

x-ray diffraction · 12 distinct chains · 20% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Leucine-rich repeat extensin-like protein 2	protein	342	19% helix, 23% strand	O48809
B	Leucine-rich repeat extensin-like protein 2	protein	328	20% helix, 23% strand	O48809
C	Leucine-rich repeat extensin-like protein 2	protein	343	19% helix, 22% strand	O48809
D	Leucine-rich repeat extensin-like protein 2	protein	336	19% helix, 21% strand	O48809
E	Leucine-rich repeat extensin-like protein 2	protein	344	21% helix, 22% strand	O48809
F	Leucine-rich repeat extensin-like protein 2	protein	336	19% helix, 21% strand	O48809
G	Leucine-rich repeat extensin-like protein 2	protein	342	19% helix, 22% strand	O48809
H	Leucine-rich repeat extensin-like protein 2	protein	325	20% helix, 20% strand	O48809
I, L, M, O	Protein ralf-like 4	protein	47	26% helix, 0% strand	Q9FZA0
J	Protein ralf-like 4	protein	46	20% helix, 0% strand	Q9FZA0
K, P	Protein ralf-like 4	protein	45	18% helix, 0% strand	Q9FZA0
N	Protein ralf-like 4	protein	46	15% helix, 0% strand	Q9FZA0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, B, I, C, D, E, F, M, G, H, O, L
BMA · beta-D-mannopyranose · sugar · 10 copies · chains B, A, D, C, F, E, G
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains F, E

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

Pockets

16 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	94	0.59	0.87	19	empty
2	207	0.52	0.77	38	empty
3	88	0.51	0.82	22	empty
4	172	0.48	0.76	27	empty
5	153	0.48	0.77	29	empty

Interfaces

15 interfaces between chains.

H–P · 1633 Å² buried · 21 hydrogen bonds · protein-protein
C–K · 1600 Å² buried · 33 hydrogen bonds · protein-protein
E–M · 1582 Å² buried · 28 hydrogen bonds · protein-protein
G–O · 1582 Å² buried · 29 hydrogen bonds · protein-protein
B–J · 1578 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 56 disulfide, 29 glycan (disulfide, N-glycosylation).

Compared structures

6QXP · Protein peptide complex · the same entry in another collection · chain K against K, 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 O48809
Every structure of UniProt Q9FZA0
Elsewhere: RCSB PDB 6QXP · PDBe 6QXP · UniProt O48809 · UniProt Q9FZA0

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