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Crystal structure of HLA-DQ2.5-CLIP1 at 2.73 resolution

Analyse Crystal structure of HLA-DQ2.5-CLIP1 at 2.73 resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KSU
Type: protein
Length: 751 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dq alpha 1 chain; MHC class II HLA-dq-beta-1…
UniProt: P01909, O19712
Pockets: 9 · best druggability 0.51

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	182	16% helix, 45% strand	P01909
B	MHC class II HLA-dq-beta-1	protein	180	20% helix, 46% strand	O19712
C, F	HLA class II histocompatibility antigen gamma chain	protein	14	0% helix, 7% strand	—
E	MHC class II HLA-dq-beta-1	protein	179	22% helix, 45% strand	O19712

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	244	0.51	0.75	35	empty
2	198	0.47	0.74	23	empty
3	199	0.46	0.74	24	empty
4	163	0.45	0.75	22	empty
5	166	0.44	0.75	20	empty

Interfaces

7 interfaces between chains.

D–E · 2654 Å² buried · 49 hydrogen bonds · protein-protein
A–B · 2611 Å² buried · 46 hydrogen bonds · protein-protein
E–F · 724 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 715 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 702 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5KSU · Crystal structure of HLA-DQ2.5-CLIP1 at 2.73 resolution · the same entry in another collection · chain F against F, TM-score 1.00
P01909 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dq alpha 1… · 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 P01909
Every structure of UniProt O19712
Elsewhere: RCSB PDB 5KSU · PDBe 5KSU · UniProt P01909 · UniProt O19712

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