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Crystal structure of SB47 TCR-HLA B*3505-lpep complex

Analyse Crystal structure of SB47 TCR-HLA B*3505-lpep complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JRY
Type: protein
Length: 832 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Trans-activator protein BZLF1; SB47 TCR alpha…
UniProt: C5MK56, P61769, Q3KSS8
Ligands: MG, NA
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 13% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	28% helix, 38% strand	C5MK56
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Trans-activator protein BZLF1	protein	13	0% helix, 0% strand	Q3KSS8
D	SB47 TCR alpha chain	protein	201	5% helix, 47% strand	—
E	SB47 TCR beta chain	protein	242	7% helix, 49% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, A
NA · Sodium ion · metal · chains B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	972	0.78	0.80	82	empty
2	585	0.69	0.78	52	MG
3	238	0.56	0.78	32	empty
4	180	0.52	0.78	32	NA
5	126	0.43	0.76	23	empty

Interfaces

6 interfaces between chains.

D–E · 2276 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1394 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 974 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 512 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 508 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4JRY · Crystal Structure of SB47 TCR-HLA B*3505-LPEP complex · the same entry in another collection · chain A against A, 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 0.98

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 C5MK56
Every structure of UniProt P61769
Every structure of UniProt Q3KSS8
Elsewhere: RCSB PDB 4JRY · PDBe 4JRY · UniProt C5MK56 · UniProt P61769 · UniProt Q3KSS8

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