MolNFT v1 · #184811 · protein

MHC I A02 allele presenting ylqlrtfll

7P3E · MHC class I antigen: “MHC I A02 allele presenting ylqlrtfll”. X-ray diffraction, 1 ligand (IOD), 8 pockets (best druggability 0.68). MolNFT v1 #184811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7P3E
Type: protein
Length: 770 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Tyr-leu-gln-leu-arg-thr-phe-leu-leu
UniProt: A0A5B8RNS7, P61769
Ligands: IOD
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	MHC class I antigen	protein	276	28% helix, 40% strand	A0A5B8RNS7
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Tyr-leu-gln-leu-arg-thr-phe-leu-leu	protein	9	0% helix, 0% strand	—

Ligands and binding sites

IOD · Iodide ion · ion · 24 copies · chains A, B, D, C, F, E
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, F

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	637	0.68	0.77	60	IOD
2	574	0.67	0.77	52	IOD
3	310	0.55	0.75	44	IOD
4	203	0.49	0.76	32	IOD
5	83	0.45	0.81	19	empty

Interfaces

6 interfaces between chains.

A–B · 1494 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1487 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 944 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 932 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 248 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7P3E · MHC I A02 Allele presenting YLQLRTFLL · the same entry in another collection · chain F against F, 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
Elsewhere: RCSB PDB 7P3E · PDBe 7P3E · UniProt A0A5B8RNS7 · UniProt P61769

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