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Crystal structure of SB27 TCR in complex with HLA-B*3508- 13MER peptide

Analyse Crystal structure of SB27 TCR in complex with HLA-B*3508- 13MER peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2AK4
Type: protein
Length: 3,329 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA-B35 variant; Beta-2-microglobulin; EBV peptide lpeplpqgqltay; SB27 T cell receptor…
UniProt: P61769
Ligands: IOD
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, K, Q	HLA-B35 variant	protein	276	27% helix, 39% strand	—
B, G, L, R	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C, H, M, S	EBV peptide lpeplpqgqltay	protein	13	0% helix, 8% strand	—
D, I, N, T	SB27 T cell receptor alpha chain	protein	204	3% helix, 45% strand	—
E, J, P	SB27 T cell receptor beta chain	protein	241	7% helix, 50% strand	—
U	SB27 T cell receptor beta chain	protein	238	7% helix, 49% strand	—

Ligands and binding sites

IOD · Iodide ion · ion · 22 copies · chains A, K, B, C, D, E, F, Q, G, H, J, L, R, S

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1050	0.81	0.83	102	empty
2	900	0.81	0.83	95	empty
3	1152	0.77	0.79	91	empty
4	1070	0.75	0.78	85	empty
5	1121	0.73	0.76	83	empty

Interfaces

43 interfaces between chains.

N–P · 2338 Å² buried · 20 hydrogen bonds · protein-protein
I–J · 2265 Å² buried · 23 hydrogen bonds · protein-protein
D–E · 2207 Å² buried · 22 hydrogen bonds · protein-protein
T–U · 2080 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 1375 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

2AK4 · Crystal Structure of SB27 TCR in complex with HLA-B*3508-13mer peptide · the same entry in another collection · chain U against U, 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 P61769
Elsewhere: RCSB PDB 2AK4 · PDBe 2AK4 · UniProt P61769

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