MolNFT v1 · #46989 · protein

Crystal structure of BM3.3 scfv TCR in complex with PBM8-H-2KBM8 MHC class I molecule

2OL3 · BM3.3 T-cell receptor alpha-chain: “Crystal structure of BM3.3 scfv TCR in complex with PBM8-H-2KBM8 MHC class I molecule”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.63). MolNFT v1 #46989 on GenesisL1: 3D…

PDB: 2OL3
Type: protein
Length: 615 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BM3.3 T-cell receptor alpha-chain; BM3.3 T-cell receptor beta-chain; Allogeneic H-2KBM8…
UniProt: Q5R1F1, P04214, P01901, P01887, Q91YE7
Ligands: NAG
Pockets: 10 · best druggability 0.63

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BM3.3 T-cell receptor alpha-chain	protein	118	3% helix, 44% strand	Q5R1F1
B	BM3.3 T-cell receptor beta-chain	protein	113	0% helix, 58% strand	P04214
H	Allogeneic H-2KBM8 MHC class I molecule	protein	276	27% helix, 38% strand	P01901
L	Beta-2-microglobulin	protein	100	0% helix, 45% strand	P01887
P	Naturally processed octapeptide PBM8	protein	8	0% helix, 0% strand	Q91YE7

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.63	0.75	55	empty
2	137	0.59	0.84	29	empty
3	84	0.51	0.83	21	empty
4	168	0.49	0.77	25	empty
5	143	0.44	0.76	30	empty

Interfaces

7 interfaces between chains.

H–L · 1258 Å² buried · 21 hydrogen bonds · protein-protein
H–P · 913 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 845 Å² buried · 14 hydrogen bonds · protein-protein
B–H · 366 Å² buried · 3 hydrogen bonds · protein-protein
A–H · 362 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2OL3 · crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule · the same entry in another collection · chain P against P, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain L against A, TM-score 0.99
P04214 · AlphaFold monomer V2.0 prediction for T-cell receptor beta chain V region E1 (P04214) · a predicted model of the same protein · chain B against A, TM-score 0.96
Q91YE7 · AlphaFold monomer V2.0 prediction for RNA-binding protein 5 (Q91YE7) · a predicted model of the same protein · chain P against A, TM-score 0.47

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 Q5R1F1
Every structure of UniProt P04214
Every structure of UniProt P01901
Every structure of UniProt P01887
Every structure of UniProt Q91YE7
Elsewhere: RCSB PDB 2OL3 · PDBe 2OL3 · UniProt Q5R1F1 · UniProt P04214 · UniProt P01901 · UniProt P01887 · UniProt Q91YE7

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