MolNFT v1 · #12249 · protein

Murine T-cell receptor variable DOMAIN/FAB complex

1KB5 · KB5-C20 T-cell antigen receptor: “Murine T-cell receptor variable DOMAIN/FAB complex”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #12249 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KB5
Type: protein
Length: 665 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KB5-C20 T-cell antigen receptor; Antibody desire-1
UniProt: P04214, P01837, P01865
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 3% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	KB5-C20 T-cell antigen receptor	protein	115	3% helix, 50% strand	—
B	KB5-C20 T-cell antigen receptor	protein	117	0% helix, 51% strand	P04214
L	Antibody desire-1	protein	214	7% helix, 48% strand	P01837
H	Antibody desire-1	protein	219	3% helix, 50% strand	P01865

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.79	0.97	31	empty
2	593	0.62	0.74	64	empty
3	78	0.50	0.84	19	empty
4	174	0.49	0.77	24	empty
5	137	0.42	0.75	26	empty

Interfaces

6 interfaces between chains.

L–H · 1905 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 951 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 460 Å² buried · 11 hydrogen bonds · protein-protein
B–H · 424 Å² buried · 2 hydrogen bonds · protein-protein
B–L · 390 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

1KB5 · Murine T-cell receptor variable DOMAIN/FAB complex · the same entry in another collection · chain A against A, TM-score 1.00
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 0.92
P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.52
P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain L against A, TM-score 0.49

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 P04214
Every structure of UniProt P01837
Every structure of UniProt P01865
Elsewhere: RCSB PDB 1KB5 · PDBe 1KB5 · UniProt P04214 · UniProt P01837 · UniProt P01865

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