MolNFT v1 · #153769 · protein

Crystal structure of peptide in complex with HLA-A1101.

6JP3 · HLA class I histocompatibility antigen, a-11 alpha chain: “Crystal structure of peptide in complex with HLA-A1101.”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #153769 on GenesisL1: 3D structure, binding sites…

PDB: 6JP3
Type: protein
Length: 382 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-11 alpha chain; Beta-2-microglobulin…
UniProt: P13746, P61769
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-11 alpha chain	protein	274	26% helix, 40% strand	P13746
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Ala-thr-ile-gly-thr	protein	5	0% helix, 0% strand	—
D	Ala-met-tyr-lys	protein	4	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, B, D

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.69	0.77	63	GOL
2	200	0.52	0.77	35	empty
3	153	0.49	0.78	23	GOL
4	107	0.48	0.80	25	GOL
5	64	0.34	0.77	16	empty

Interfaces

3 interfaces between chains.

A–B · 1303 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 471 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 406 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6JP3 · Crystal structure of peptide in complex with HLA-A1101. · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P13746
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6JP3 · PDBe 6JP3 · UniProt P13746 · UniProt P61769

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