MolNFT v1 · #162984 · protein

Crystal structure of the T-cell receptor NYE_S3 bound to HLA A2*01- sllmwitqv

6RP9 · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structure of the T-cell receptor NYE_S3 bound to HLA A2*01- sllmwitqv”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #162984 on GenesisL1: 3D…

PDB: 6RP9
Type: protein
Length: 2,081 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
UniProt: P01892, P61769, P78358
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 8% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	26% helix, 38% strand	P01892
B, G	Beta-2-microglobulin	protein	100	0% helix, 47% strand	P61769
C, H	CANCER/TESTIS antigen 1	protein	9	0% helix, 0% strand	P78358
D	T-cell receptor alpha chain	protein	197	2% helix, 46% strand	—
E, J	T-cell receptor beta chain	protein	244	7% helix, 48% strand	—
I	T-cell receptor alpha chain	protein	198	2% helix, 46% strand	—
K	T-cell receptor alpha chain	protein	187	2% helix, 47% strand	—
L	T-cell receptor beta chain	protein	243	7% helix, 49% strand	—

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	864	0.73	0.78	79	empty
2	1015	0.73	0.76	79	empty
3	1189	0.73	0.76	76	empty
4	622	0.70	0.79	57	empty
5	748	0.70	0.77	64	empty

Interfaces

16 interfaces between chains.

I–J · 2093 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 2087 Å² buried · 31 hydrogen bonds · protein-protein
K–L · 1967 Å² buried · 26 hydrogen bonds · protein-protein
F–G · 1499 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1461 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

6RP9 · Crystal structure of the T-cell receptor NYE_S3 bound to HLA A2*01-SLLMWITQV · the same entry in another collection · chain L against L, TM-score 1.00

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 P01892
Every structure of UniProt P61769
Every structure of UniProt P78358
Elsewhere: RCSB PDB 6RP9 · PDBe 6RP9 · UniProt P01892 · UniProt P61769 · UniProt P78358

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