MolNFT v1 · #15167 · protein

2C/H-2KBM3/DEV8 allogeneic complex

1MWA · 2C T cell receptor alpha chain: “2C/H-2KBM3/DEV8 allogeneic complex”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.79). MolNFT v1 #15167 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1MWA
Type: protein
Length: 1,640 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2C T cell receptor alpha chain; 2C T cell receptor beta chain; H-2KBM3 MHC class I…
UniProt: P01901, P01887, Q62425
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	2C T cell receptor alpha chain	protein	202	3% helix, 41% strand	—
B, D	2C T cell receptor beta chain	protein	237	6% helix, 50% strand	—
H, I	H-2KBM3 MHC class I molecule heavy chain	protein	274	27% helix, 40% strand	P01901
L, M	Microglobulin MHC light chain	protein	99	0% helix, 49% strand	P01887
P, Q	DEV8	protein	8	0% helix, 0% strand	Q62425

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C, B, H
BMA · beta-D-mannopyranose · sugar · 3 copies
GOL · Glycerol · additive · 3 copies · chains A, B, I, H, L
ACY · Acetic acid · additive · chains A, H, P

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1083	0.79	0.81	116	empty
2	1003	0.73	0.76	81	empty
3	720	0.72	0.79	64	ACY
4	74	0.72	0.96	21	empty
5	767	0.71	0.77	65	empty

Interfaces

17 interfaces between chains.

A–B · 2289 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2081 Å² buried · 21 hydrogen bonds · protein-protein
I–M · 1228 Å² buried · 20 hydrogen bonds · protein-protein
H–L · 1187 Å² buried · 20 hydrogen bonds · protein-protein
H–P · 912 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

1MWA · 2C/H-2KBM3/DEV8 allogeneic complex · the same entry in another collection · chain Q against Q, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain L 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 P01901
Every structure of UniProt P01887
Every structure of UniProt Q62425
Elsewhere: RCSB PDB 1MWA · PDBe 1MWA · UniProt P01901 · UniProt P01887 · UniProt Q62425

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