MolNFT v1 · #157371 · protein

Recognition of MHC-like molecule

6MWR · Major histocompatibility complex class I-related gene…: “Recognition of MHC-like molecule”. X-ray diffraction, 2 ligands (2LJ, NAG), 14 pockets (best druggability 0.81). MolNFT v1 #157371 on GenesisL1: 3D structure, binding sites…

PDB: 6MWR
Type: protein
Length: 789 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I-related gene protein; Beta-2-microglobulin; G7…
UniProt: Q95460, P61769
Ligands: 2LJ, NAG
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex class I-related gene protein	protein	265	28% helix, 38% strand	Q95460
B	Beta-2-microglobulin	protein	97	0% helix, 49% strand	P61769
C	G7 gamma chain T cell receptor	protein	222	5% helix, 45% strand	—
D	Delta chain of T cell receptor	protein	205	0% helix, 50% strand	—

Ligands and binding sites

2LJ · 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1144	0.81	0.82	107	empty
2	83	0.72	0.96	27	empty
3	63	0.69	0.95	14	empty
4	277	0.68	0.83	37	2LJ
5	211	0.60	0.81	37	empty

Interfaces

5 interfaces between chains.

C–D · 1773 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1159 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 925 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 202 Å² buried · 1 hydrogen bond · protein-protein
B–D · 19 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

6MWR · Recognition of MHC-like molecule · the same entry in another collection · chain A against A, 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 0.97

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 Q95460
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6MWR · PDBe 6MWR · UniProt Q95460 · UniProt P61769

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