Research workbench

Crystal structure of chicken MHC class II for 1.9 ångström

Analyse Crystal structure of chicken MHC class II for 1.9 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KVM
Type: protein
Length: 380 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class II alpha chain; MHC class II beta chain 2; Peptide from 60S ribosomal protein…
UniProt: Q4U5Z6, Q4U600, P67883
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class II alpha chain	protein	184	16% helix, 46% strand	Q4U5Z6
B	MHC class II beta chain 2	protein	179	20% helix, 46% strand	Q4U600
C	Peptide from 60S ribosomal protein L30	protein	17	0% helix, 6% strand	P67883

Ligands and binding sites

GOL · Glycerol · additive · chains A, B

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

Pockets

4 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	169	0.56	0.81	30	empty
2	85	0.38	0.76	19	empty
3	80	0.32	0.74	19	empty
4	73	0.31	0.74	25	empty

Interfaces

3 interfaces between chains.

A–B · 2707 Å² buried · 45 hydrogen bonds · protein-protein
B–C · 713 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 673 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6KVM · Crystal structure of Chicken MHC Class II for 1.9 angstrom · the same entry in another collection · chain A against A, TM-score 1.00
P67883 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L30 (P67883) · a predicted model of the same protein · chain C against A, TM-score 0.27

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 Q4U5Z6
Every structure of UniProt Q4U600
Every structure of UniProt P67883
Elsewhere: RCSB PDB 6KVM · PDBe 6KVM · UniProt Q4U5Z6 · UniProt Q4U600 · UniProt P67883

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