MolNFT v1 · #171580 · protein

Human class I major histocompatibility complex, A02 allele, presenting lls (T-BUTYL)Y fgtpt

6Z9X · MHC class I antigen: “Human class I major histocompatibility complex, A02 allele, presenting lls (T-BUTYL)Y fgtpt”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.71). MolNFT v1 #171580 on GenesisL1: 3D structure…

PDB: 6Z9X
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; Leu-leu-ser-tur-phe-gly-thr-pro-thr
UniProt: A0A5B8RNS7, P61769
Ligands: SO4
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	MHC class I antigen	protein	276	26% helix, 39% strand	A0A5B8RNS7
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Leu-leu-ser-tur-phe-gly-thr-pro-thr	protein	9	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, E

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

Pockets

8 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	628	0.71	0.79	57	empty
2	684	0.70	0.78	64	empty
3	69	0.47	0.83	22	SO4
4	99	0.46	0.80	25	empty
5	96	0.43	0.79	19	empty

Interfaces

6 interfaces between chains.

A–B · 1468 Å² buried · 26 hydrogen bonds · protein-protein
D–E · 1423 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 854 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 847 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 68 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

6Z9X · Human Class I Major Histocompatibility Complex, A02 allele, presenting LLS (t-butyl)Y… · 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 6Z9X · PDBe 6Z9X · UniProt A0A5B8RNS7 · UniProt P61769

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