MolNFT v1 · #27407 · protein

Crystal structure of human CD3-E/D dimer in complex with a UCHT1 single-chain antibody fragment

1XIW · T-cell surface glycoprotein CD3 epsilon chain: “Crystal structure of human CD3-E/D dimer in complex with a UCHT1 single-chain antibody fragment”. X-ray diffraction, 7 pockets (best druggability 0.53). MolNFT v1 #27407 on GenesisL1…

PDB: 1XIW
Type: protein
Length: 765 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell surface glycoprotein CD3 epsilon chain; T-cell surface glycoprotein CD3 delta…
UniProt: P07766, P04234
Pockets: 7 · best druggability 0.53

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-cell surface glycoprotein CD3 epsilon chain	protein	91	8% helix, 44% strand	P07766
B	T-cell surface glycoprotein CD3 delta chain	protein	66	9% helix, 58% strand	P04234
C, G	Immunoglobulin light chain variable region	protein	107	3% helix, 48% strand	—
D, H	Immunoglobulin heavy chain variable region	protein	122	7% helix, 53% strand	—
E	T-cell surface glycoprotein CD3 epsilon chain	protein	87	8% helix, 46% strand	P07766
F	T-cell surface glycoprotein CD3 delta chain	protein	63	10% helix, 60% strand	P04234

Pockets

7 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	301	0.53	0.75	36	empty
2	296	0.50	0.73	41	empty
3	127	0.38	0.73	25	empty
4	104	0.36	0.74	26	empty
5	73	0.31	0.74	21	empty

Interfaces

12 interfaces between chains.

A–B · 1012 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 919 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 882 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 871 Å² buried · 8 hydrogen bonds · protein-protein
E–H · 682 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

1XIW · Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody… · the same entry in another collection · chain H against H, TM-score 1.00
P07766 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 epsilon chain… · a predicted model of the same protein · chain E against A, TM-score 0.97
P04234 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 delta chain (P04234) · a predicted model of the same protein · chain F against A, TM-score 0.94

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 P07766
Every structure of UniProt P04234
Elsewhere: RCSB PDB 1XIW · PDBe 1XIW · UniProt P07766 · UniProt P04234

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