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Crystal Structure of IAg7 in complex with RLGL-WE14

Analyse Crystal Structure of IAg7 in complex with RLGL-WE14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DMK
Type: protein
Length: 1,445 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.45
Source: Mus musculus
Molecule: H-2 class II histocompatibility antigen, A-D alpha chain; beta chain of Major…
UniProt: P04228, Q31135
Pockets: 17 · best druggability 0.85

Structure

x-ray diffraction · resolution 2.45 · 5 distinct chains · 16% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class II histocompatibility antigen, A-D alpha chain	protein	171	12% helix, 44% strand	P04228
B, F	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein	protein	190	19% helix, 45% strand	Q31135
C, E, G	H-2 class II histocompatibility antigen, A-D alpha chain	protein	173	12% helix, 43% strand	P04228
D	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein	protein	186	19% helix, 38% strand	Q31135
H	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein	protein	189	19% helix, 44% strand	Q31135

Ligands and binding sites

FLC · Citrate anion · additive · 2 copies · chains B, F

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1153	0.85	0.86	92	empty
2	1186	0.84	0.85	104	empty
3	1127	0.78	0.80	124	empty
4	140	0.64	0.86	22	empty
5	419	0.59	0.75	48	empty

Interfaces

15 interfaces between chains.

E–F · 3013 Å² buried · 60 hydrogen bonds · protein-protein
G–H · 3001 Å² buried · 62 hydrogen bonds · protein-protein
A–B · 2984 Å² buried · 61 hydrogen bonds · protein-protein
C–D · 2928 Å² buried · 58 hydrogen bonds · protein-protein
E–G · 638 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5DMK · Crystal structure of IAG7 in complex with rlgl-WE14 · the same entry in another collection · chain H against H, TM-score 1.00
P04228 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P04228
Every structure of UniProt Q31135
Elsewhere: RCSB PDB 5DMK · PDBe 5DMK · UniProt P04228 · UniProt Q31135

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