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Cystal structure of rhesus macaque MHC class I:MAMU-A*02

Analyse Cystal structure of rhesus macaque MHC class I:MAMU-A*02 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JTT
Type: protein
Length: 1,155 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I mamu-A*02; Beta-2-microglobulin; Peptide of protein nef
UniProt: Q30597, Q6V7J5, Q9WH73
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G	MHC class I mamu-A*02	protein	276	25% helix, 39% strand	Q30597
B, E, H	Beta-2-microglobulin	protein	100	0% helix, 49% strand	Q6V7J5
C, F, I	Peptide of protein nef	protein	9	0% helix, 0% strand	Q9WH73

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	684	0.78	0.83	91	empty
2	574	0.76	0.83	69	empty
3	523	0.74	0.82	63	empty
4	218	0.70	0.87	22	empty
5	223	0.58	0.80	35	empty

Interfaces

12 interfaces between chains.

D–E · 1393 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1391 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1388 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 889 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 888 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3JTT · Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 · the same entry in another collection · chain I against I, TM-score 1.00
Q6V7J5 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q6V7J5) · a predicted model of the same protein · chain E 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 Q30597
Every structure of UniProt Q6V7J5
Every structure of UniProt Q9WH73
Elsewhere: RCSB PDB 3JTT · PDBe 3JTT · UniProt Q30597 · UniProt Q6V7J5 · UniProt Q9WH73

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