MolNFT v1 · #30066 · protein

Crystal structure of the murine MHC class ib molecule M10.5

1ZS8 · Histocompatibility 2, M region locus 10.5: “Crystal structure of the murine MHC class ib molecule M10.5”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.75). MolNFT v1 #30066 on GenesisL1: 3D structure, binding…

PDB: 1ZS8
Type: protein
Length: 1,800 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histocompatibility 2, M region locus 10.5; Beta-2-microglobulin
UniProt: P61769
Ligands: NAG
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I	Histocompatibility 2, M region locus 10.5	protein	261	25% helix, 38% strand	—
B, D, F, H, J	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, E, G, I

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1160	0.75	0.78	130	empty
2	583	0.66	0.76	50	empty
3	609	0.66	0.76	54	empty
4	555	0.66	0.77	51	empty
5	567	0.66	0.76	52	empty

Interfaces

11 interfaces between chains.

A–B · 1244 Å² buried · 13 hydrogen bonds · protein-protein
I–J · 1244 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 1240 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1239 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1237 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

1ZS8 · Crystal Structure of the Murine MHC Class Ib Molecule M10.5 · 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 J 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 P61769
Elsewhere: RCSB PDB 1ZS8 · PDBe 1ZS8 · UniProt P61769

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