MolNFT v1 · #156977 · protein

5287 TCR bound to iab PADI4

6MKR · H-2 class II histocompatibility antigen, a-B alpha chain: “5287 TCR bound to iab PADI4”. X-ray diffraction, 11 pockets (best druggability 0.63). MolNFT v1 #156977 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MKR
Type: protein
Length: 808 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; Padi 4 (92-105) peptide and MHC…
EC: 3.5.3.15
UniProt: P14434, Q9Z183, P14483
Pockets: 11 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	H-2 class II histocompatibility antigen, a-B alpha chain	protein	174	15% helix, 40% strand	P14434
D	Padi 4 (92-105) peptide and MHC class II iab beta chain (EC 3.5.3.15)	protein	201	18% helix, 41% strand	Q9Z183, P14483
A	5287 TCR alpha chain	protein	195	7% helix, 42% strand	—
B	5287 TCR beta chain	protein	238	7% helix, 51% strand	—

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	244	0.63	0.82	37	empty
2	463	0.60	0.75	53	empty
3	58	0.59	0.91	24	empty
4	228	0.51	0.76	36	empty
5	234	0.50	0.75	39	empty

Interfaces

6 interfaces between chains.

C–D · 2944 Å² buried · 55 hydrogen bonds · protein-protein
A–B · 1779 Å² buried · 20 hydrogen bonds · protein-protein
C–B · 381 Å² buried · 3 hydrogen bonds · protein-protein
D–A · 191 Å² buried · 2 hydrogen bonds · protein-protein
D–B · 189 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6MKR · 5287 TCR bound to IAb 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 0.73
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 6MKR · PDBe 6MKR · UniProt P14434 · UniProt Q9Z183 · UniProt P14483

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