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Crystal structure of SB27 TCR in complex with the 'restriction triad' mutant HLA-B*3508-13MER

Analyse Crystal structure of SB27 TCR in complex with the 'restriction triad' mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KXF
Type: protein
Length: 3,332 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin; SB27 T…
UniProt: P30685, P61769, P03206
Ligands: IOD
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, K, I	HLA class I histocompatibility antigen, B-35 alpha chain	protein	276	27% helix, 38% strand	P30685
B, F, L, J	Beta-2-microglobulin	protein	99	0% helix, 52% strand	P61769
D, G, N, M	SB27 T cell receptor alpha chain	protein	204	1% helix, 43% strand	—
E, H, P, O	SB27 T cell receptor beta chain	protein	241	8% helix, 47% strand	—
Q, R, T, S	Peptide from trans-activator protein BZLF1	protein	13	0% helix, 8% strand	P03206

Ligands and binding sites

IOD · Iodide ion · ion · 24 copies · chains A, B, C, I, D, E, F, G, H, K, L, N, P, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1118	0.84	0.85	110	empty
2	942	0.82	0.83	90	IOD
3	932	0.77	0.80	90	empty
4	1038	0.77	0.79	77	empty
5	720	0.76	0.81	63	IOD

Interfaces

46 interfaces between chains.

N–P · 2333 Å² buried · 23 hydrogen bonds · protein-protein
D–E · 2278 Å² buried · 19 hydrogen bonds · protein-protein
M–O · 2276 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 2259 Å² buried · 29 hydrogen bonds · protein-protein
K–L · 1353 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

3KXF · Crystal Structure of SB27 TCR in complex with the 'restriction triad' mutant… · the same entry in another collection · chain S against S, 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 P30685
Every structure of UniProt P61769
Every structure of UniProt P03206
Elsewhere: RCSB PDB 3KXF · PDBe 3KXF · UniProt P30685 · UniProt P61769 · UniProt P03206

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