MolNFT v1 · #10320 · protein

Structure of minor histocompatibility antigen peptide, H13A, complexed to H2-db

1INQ · H-2 class I histocompatibility antigen, D-B alpha chain: “Structure of minor histocompatibility antigen peptide, H13A, complexed to H2-db”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #10320 on GenesisL1: 3D…

PDB: 1INQ
Type: protein
Length: 383 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2 microglobulin; MHC class…
UniProt: P01899, P01887, Q9D8V0
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	275	27% helix, 40% strand	P01899
B	Beta-2 microglobulin	protein	99	0% helix, 49% strand	P01887
C	MHC class I H13A minor histocompatibility peptide	protein	9	0% helix, 0% strand	Q9D8V0

Ligands and binding sites

DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

3 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	581	0.63	0.75	57	DMS
2	144	0.44	0.76	28	empty
3	83	0.38	0.77	18	empty

Interfaces

2 interfaces between chains.

A–B · 1312 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 878 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1INQ · Structure of Minor Histocompatibility Antigen peptide, H13a, complexed to H2-Db · the same entry in another collection · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q9D8V0 · AlphaFold monomer V2.0 prediction for minor histocompatibility antigen H13 (Q9D8V0) · a predicted model of the same protein · chain C against A, TM-score 0.38

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 P01899
Every structure of UniProt P01887
Every structure of UniProt Q9D8V0
Elsewhere: RCSB PDB 1INQ · PDBe 1INQ · UniProt P01899 · UniProt P01887 · UniProt Q9D8V0

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