Research workbench
Il-2 mutant D10 ternary complex
Analyse Il-2 mutant D10 ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QAZ
- Type
- protein
- Length
- 6,076 residues
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-2; Interleukin-2 receptor subunit beta; Cytokine receptor common subunit gamma
- UniProt
- P60568, P14784, P31785
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 9 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S, V, e, h | Interleukin-2 | protein | 121 | 61% helix, 8% strand | P60568 |
| B, N, Q | Interleukin-2 receptor subunit beta | protein | 195 | 3% helix, 49% strand | P14784 |
| C, I | Cytokine receptor common subunit gamma | protein | 188 | 3% helix, 46% strand | P31785 |
| E, H, K, T, W, Z, c, f, i | Interleukin-2 receptor subunit beta | protein | 196 | 3% helix, 49% strand | P14784 |
| F | Cytokine receptor common subunit gamma | protein | 186 | 3% helix, 44% strand | P31785 |
| L, O, U, X, a, d, g, j | Cytokine receptor common subunit gamma | protein | 191 | 3% helix, 43% strand | P31785 |
| R | Cytokine receptor common subunit gamma | protein | 188 | 3% helix, 45% strand | P31785 |
| Y | Interleukin-2 | protein | 120 | 65% helix, 8% strand | P60568 |
| b | Interleukin-2 | protein | 119 | 61% helix, 3% strand | P60568 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains B, C, Z, E, F, c, H, I, K, L, N, O, i, Q, R, T, U, W, X, a, d, f, g, j
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.65 | 0.77 | 57 | empty |
| 2 | 70 | 0.64 | 0.92 | 22 | empty |
| 3 | 401 | 0.63 | 0.78 | 47 | empty |
| 4 | 330 | 0.61 | 0.78 | 44 | empty |
| 5 | 370 | 0.61 | 0.77 | 45 | empty |
Interfaces
46 interfaces between chains.
- T–U · 1035 Ų buried · 19 hydrogen bonds · protein-protein
- Z–a · 997 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 988 Ų buried · 14 hydrogen bonds · protein-protein
- W–X · 987 Ų buried · 21 hydrogen bonds · protein-protein
- i–j · 977 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 disulfide (disulfide).
Compared structures
- 3QAZ · IL-2 mutant D10 ternary complex · the same entry in another collection · chain G against G, TM-score 1.00
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 P60568
- Every structure of UniProt P14784
- Every structure of UniProt P31785
- Elsewhere: RCSB PDB 3QAZ · PDBe 3QAZ · UniProt P60568 · UniProt P14784 · UniProt P31785
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