MolNFT v1 · #156964 · protein

4699 TCR bound to I-ab PADI4

6MKD · H-2 class II histocompatibility antigen, a-B alpha chain: “4699 TCR bound to I-ab PADI4”. X-ray diffraction, 12 pockets (best druggability 0.66). MolNFT v1 #156964 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MKD
Type: protein
Length: 799 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class II histocompatibility antigen, a-B alpha chain; PADI4 (92-105) peptide and MHC…
EC: 3.5.3.15
UniProt: P14434, Q9Z183, P14483
Pockets: 12 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	H-2 class II histocompatibility antigen, a-B alpha chain	protein	166	16% helix, 39% strand	P14434
D	PADI4 (92-105) peptide and MHC class II I-ab beta CHAIN,H-2 class II histocompatibility antigen, a beta chain (EC 3.5.3.15)	protein	201	17% helix, 40% strand	Q9Z183, P14483
A	4699 TCR alpha chain	protein	193	5% helix, 42% strand	—
B	4699 TCR beta chain	protein	239	6% helix, 49% strand	—

Pockets

12 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	271	0.66	0.83	43	empty
2	428	0.58	0.74	49	empty
3	269	0.52	0.75	42	empty
4	149	0.48	0.77	21	empty
5	184	0.46	0.75	33	empty

Interfaces

6 interfaces between chains.

C–D · 2923 Å² buried · 55 hydrogen bonds · protein-protein
A–B · 1785 Å² buried · 22 hydrogen bonds · protein-protein
C–B · 419 Å² buried · 6 hydrogen bonds · protein-protein
D–A · 193 Å² buried · 5 hydrogen bonds · protein-protein
D–B · 186 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6MKD · 4699 TCR bound to I-Ab Padi4 · the same entry in another collection · chain C against C, TM-score 1.00
P14434 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-B alpha… · a predicted model of the same protein · chain C against A, TM-score 0.94
P14483 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a beta… · a predicted model of the same protein · chain D against A, TM-score 0.74
Q9Z183 · AlphaFold monomer V2.0 prediction for protein-arginine deiminase type-4 (Q9Z183) · a predicted model of the same protein · chain D against A, TM-score 0.40

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 P14434
Every structure of UniProt Q9Z183
Every structure of UniProt P14483
Elsewhere: RCSB PDB 6MKD · PDBe 6MKD · UniProt P14434 · UniProt Q9Z183 · UniProt P14483

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