MolNFT v1 · #138474 · protein

D30 TCR in complex with HLA-A*11:01-GTS1

5WKF · HLA class I histocompatibility antigen, a-11 alpha chain: “D30 TCR in complex with HLA-A*11:01-GTS1”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #138474 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5WKF
Type: protein
Length: 1,651 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-11 alpha chain; Beta-2-microglobulin; GTS1…
UniProt: P13746, P61769, A0A087WSZ9, K7N5N2
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 10% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	HLA class I histocompatibility antigen, a-11 alpha chain	protein	274	25% helix, 41% strand	P13746
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C, H	GTS1 peptide	protein	10	0% helix, 10% strand	—
D, I	T-cell receptor alpha variable 30,T-cell receptor, SP3.4 alpha chain chimera	protein	198	2% helix, 43% strand	A0A087WSZ9, K7N5N2
E, J	D30 TCR beta chain	protein	244	7% helix, 49% strand	—
G	Beta-2-microglobulin	protein	100	0% helix, 46% strand	P61769

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	1100	0.82	0.83	129	empty
2	888	0.75	0.79	71	empty
3	971	0.74	0.77	77	empty
4	908	0.72	0.77	84	empty
5	820	0.71	0.77	76	empty

Interfaces

20 interfaces between chains.

I–J · 2310 Å² buried · 28 hydrogen bonds · protein-protein
D–E · 2186 Å² buried · 19 hydrogen bonds · protein-protein
F–G · 1424 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1349 Å² buried · 26 hydrogen bonds · protein-protein
F–H · 856 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5WKF · D30 TCR in complex with HLA-A*11:01-GTS1 · the same entry in another collection · chain J against J, 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 0.99

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 P13746
Every structure of UniProt P61769
Every structure of UniProt A0A087WSZ9
Every structure of UniProt K7N5N2
Elsewhere: RCSB PDB 5WKF · PDBe 5WKF · UniProt P13746 · UniProt P61769 · UniProt A0A087WSZ9 · UniProt K7N5N2

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