MolNFT v1 · #12842 · protein

Crystal structure of class II MHC molecule iek bound to pigeon cytochrome C peptide

1KTD · H-2 class II histocompatibility antigen, E-D alpha chain: “Crystal structure of class II MHC molecule iek bound to pigeon cytochrome C peptide”. X-ray diffraction, 2 ligands (NAG, SO4), 10 pockets (best druggability 0.75). MolNFT v1…

PDB: 1KTD
Type: protein
Length: 794 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class II histocompatibility antigen, E-D alpha chain; Fusion protein consisting of…
UniProt: P01904, P00021, Q31163
Ligands: NAG, SO4
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	H-2 class II histocompatibility antigen, E-D alpha chain	protein	182	14% helix, 45% strand	P01904
B, D	Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-K	protein	215	17% helix, 38% strand	P00021, Q31163

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, C
SO4 · Sulfate ion · ion · chains B, D

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	305	0.75	0.87	30	empty
2	363	0.73	0.85	30	empty
3	154	0.68	0.89	27	SO4
4	113	0.65	0.89	20	empty
5	105	0.65	0.90	20	empty

Interfaces

5 interfaces between chains.

C–D · 3510 Å² buried · 66 hydrogen bonds · protein-protein
A–B · 3435 Å² buried · 69 hydrogen bonds · protein-protein
B–D · 910 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 208 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 204 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

1KTD · Crystal structure of class II MHC molecule iek bound to pigeon cytochrome C peptide · the same entry in another collection · chain A against A, TM-score 1.00
P01904 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, E-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
P00021 · AlphaFold monomer V2.0 prediction for cytochrome C (P00021) · a predicted model of the same protein · chain B against A, TM-score 0.21

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 P01904
Every structure of UniProt P00021
Every structure of UniProt Q31163
Elsewhere: RCSB PDB 1KTD · PDBe 1KTD · UniProt P01904 · UniProt P00021 · UniProt Q31163

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