MolNFT v1 · #184810 · protein

MHC I A02 allele presenting ylqprtfll

7P3D · MHC class I antigen: “MHC I A02 allele presenting ylqprtfll”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.69). MolNFT v1 #184810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7P3D
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Spike glycoprotein
UniProt: A0A5B8RNS7, P61769, P0DTC2
Ligands: CA
Pockets: 4 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	27% helix, 40% strand	A0A5B8RNS7
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Spike glycoprotein	protein	9	0% helix, 0% strand	P0DTC2

Ligands and binding sites

CA · Calcium ion · metal · chains B
EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B
ACT · Acetate ion · additive · chains A

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	680	0.69	0.77	55	EDO
2	99	0.46	0.80	19	EDO
3	76	0.42	0.80	17	EDO
4	56	0.33	0.77	15	empty

Interfaces

2 interfaces between chains.

A–B · 1362 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 862 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7P3D · MHC I A02 Allele presenting YLQPRTFLL · 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 A0A5B8RNS7
Every structure of UniProt P61769
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 7P3D · PDBe 7P3D · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P0DTC2

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