MolNFT v1 · #153070 · protein

The structure of HLA-A*3003/NP44

6J2A: “The structure of HLA-A*3003/NP44”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #153070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6J2A
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA-A*3003; Beta-2-microglobulin; NP44
UniProt: P61769
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA-A*3003	protein	274	27% helix, 40% strand	—
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	NP44	protein	9	0% helix, 0% strand	—

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	629	0.67	0.76	57	empty
2	107	0.42	0.77	19	empty
3	85	0.37	0.76	19	empty
4	55	0.34	0.78	17	empty

Interfaces

2 interfaces between chains.

A–B · 1280 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 887 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6J2A · The structure of HLA-A*3003/NP44 · 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 P61769
Elsewhere: RCSB PDB 6J2A · PDBe 6J2A · UniProt P61769

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