MolNFT v1 · #157071 · protein
6256 TCR bound to I-ab PADI4
6MNM · H-2 class II histocompatibility antigen, a-B alpha chain: “6256 TCR bound to I-ab PADI4”. X-ray diffraction, 9 pockets (best druggability 0.67). MolNFT v1 #157071 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MNM
- 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; PADI4 (92-105) peptide and MHC…
- EC
- 3.5.3.15
- UniProt
- P14434, Q9Z183, P14483
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | H-2 class II histocompatibility antigen, a-B alpha chain | protein | 179 | 15% helix, 43% strand | P14434 |
| D | PADI4 (92-105) peptide and MHC class II I-ab beta chain (EC 3.5.3.15) | protein | 194 | 19% helix, 44% strand | Q9Z183, P14483 |
| A | 6256 TCR alpha chain | protein | 196 | 5% helix, 44% strand | — |
| B | 6256 TCR beta chain | protein | 239 | 7% helix, 50% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.67 | 0.84 | 41 | empty |
| 2 | 741 | 0.66 | 0.74 | 80 | empty |
| 3 | 159 | 0.49 | 0.78 | 23 | empty |
| 4 | 122 | 0.44 | 0.78 | 21 | empty |
| 5 | 158 | 0.42 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2764 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2005 Ų buried · 21 hydrogen bonds · protein-protein
- C–B · 417 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 214 Ų buried · 3 hydrogen bonds · protein-protein
- D–B · 189 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MNM · 6256 TCR bound to I-Ab Padi4 · the same entry in another collection · chain D against D, 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 0.95
- 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 6MNM · PDBe 6MNM · UniProt P14434 · UniProt Q9Z183 · UniProt P14483
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