Research workbench

Rhesus macaque MHC class I molecule mamu-B*17-IW11

Analyse Rhesus macaque MHC class I molecule mamu-B*17-IW11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RWD
Type: protein
Length: 772 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I; Beta-2-microglobulin; Nef IW11 peptide from…
UniProt: Q9GJ77, Q6V7J5, Q5QGG3
Pockets: 12 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Major histocompatibility complex class I	protein	276	26% helix, 39% strand	Q9GJ77
B, E	Beta-2-microglobulin	protein	99	0% helix, 52% strand	Q6V7J5
C, F	Nef IW11 peptide from protein nef	protein	11	0% helix, 0% strand	Q5QGG3

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	537	0.72	0.81	70	empty
2	492	0.70	0.81	53	empty
3	209	0.62	0.83	32	empty
4	128	0.51	0.81	30	empty
5	122	0.48	0.79	20	empty

Interfaces

5 interfaces between chains.

D–E · 1401 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1398 Å² buried · 24 hydrogen bonds · protein-protein
D–F · 1160 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1157 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 739 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3RWD · rhesus macaque MHC class I molecule Mamu-B*17-IW11 · the same entry in another collection · chain F against F, TM-score 1.00
Q6V7J5 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q6V7J5) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q9GJ77
Every structure of UniProt Q6V7J5
Every structure of UniProt Q5QGG3
Elsewhere: RCSB PDB 3RWD · PDBe 3RWD · UniProt Q9GJ77 · UniProt Q6V7J5 · UniProt Q5QGG3

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