MolNFT v1 · #157066 · protein
4738 TCR bound to iab PADI4
6MNG · H-2 class II histocompatibility antigen, a-B alpha chain: “4738 TCR bound to iab PADI4”. X-ray diffraction, 10 pockets (best druggability 0.72). MolNFT v1 #157066 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MNG
- Type
- protein
- Length
- 805 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…
- EC
- 3.5.3.15
- UniProt
- P14434, Q9Z183, P14483
- Pockets
- 10 · best druggability 0.72
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 | 174 | 16% helix, 44% strand | P14434 |
| D | PADI4 (92-105) peptide and mhcii I-ab beta chain (EC 3.5.3.15) | protein | 193 | 21% helix, 44% strand | Q9Z183, P14483 |
| A | 4738 TCR alpha chain | protein | 199 | 3% helix, 43% strand | — |
| B | 4738 TCR beta chain | protein | 239 | 8% helix, 52% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.72 | 0.77 | 81 | empty |
| 2 | 196 | 0.64 | 0.84 | 37 | empty |
| 3 | 153 | 0.51 | 0.79 | 22 | empty |
| 4 | 82 | 0.43 | 0.80 | 15 | empty |
| 5 | 131 | 0.43 | 0.76 | 32 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2811 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 2123 Ų buried · 27 hydrogen bonds · protein-protein
- C–B · 422 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 196 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 194 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MNG · 4738 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 0.75
- 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 0.39
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 6MNG · PDBe 6MNG · UniProt P14434 · UniProt Q9Z183 · UniProt P14483
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.