MolNFT v1 · #57898 · protein

Crystal structure of a human major histocompatibilty complex

3AM8 · HLA class I histocompatibility antigen, alpha chain E: “Crystal structure of a human major histocompatibilty complex”. X-ray diffraction, 7 pockets (best druggability 0.69). MolNFT v1 #57898 on GenesisL1: 3D structure, binding sites…

PDB: 3AM8
Type: protein
Length: 770 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, alpha chain E; Beta-2-microglobulin; Peptide from…
UniProt: P13747, P61769, Q0QI92
Pockets: 7 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HLA class I histocompatibility antigen, alpha chain E	protein	276	26% helix, 39% strand	P13747
C, D	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
E, F	Peptide from glycoprotein	protein	9	0% helix, 0% strand	Q0QI92

Pockets

7 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	517	0.69	0.79	48	empty
2	689	0.69	0.76	61	empty
3	473	0.68	0.79	49	empty
4	78	0.45	0.81	15	empty
5	110	0.43	0.77	21	empty

Interfaces

5 interfaces between chains.

A–C · 1438 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1413 Å² buried · 22 hydrogen bonds · protein-protein
A–E · 888 Å² buried · 14 hydrogen bonds · protein-protein
B–F · 880 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 193 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3AM8 · Crystal Structure of a Human Major Histocompatibilty complex · 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 D against A, TM-score 0.99
P13747 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P13747
Every structure of UniProt P61769
Every structure of UniProt Q0QI92
Elsewhere: RCSB PDB 3AM8 · PDBe 3AM8 · UniProt P13747 · UniProt P61769 · UniProt Q0QI92

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