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Trimer-to-monomer disruption of tumor necrosis factor-alpha (TNF- alpha) by unnatural ALPHA/BETA-peptide-1
Analyse Trimer-to-monomer disruption of tumor necrosis factor-alpha (TNF- alpha) by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TA6
- Type
- protein
- Length
- 1,320 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor; ALPHA/BETA-peptide-1
- UniProt
- P01375
- Ligands
- XCP, K, NH2
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 9 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 141 | 0% helix, 50% strand | P01375 |
| B | Tumor necrosis factor | protein | 129 | 5% helix, 50% strand | P01375 |
| C | Tumor necrosis factor | protein | 138 | 4% helix, 49% strand | P01375 |
| D | Tumor necrosis factor | protein | 145 | 8% helix, 52% strand | P01375 |
| E | Tumor necrosis factor | protein | 136 | 2% helix, 51% strand | P01375 |
| F | Tumor necrosis factor | protein | 138 | 4% helix, 52% strand | P01375 |
| G | Tumor necrosis factor | protein | 138 | 2% helix, 51% strand | P01375 |
| H | Tumor necrosis factor | protein | 131 | 5% helix, 54% strand | P01375 |
| I, J, K, L, M, N, O, P | ALPHA/BETA-peptide-1 | protein | 28 | 71% helix, 0% strand | — |
Ligands and binding sites
- XCP · (1S,2S)-2-aminocyclopentanecarboxylic acid · ligand · 8 copies · chains I, J, M, K, N, L, O, P
- K · Potassium ion · metal · chains H
- NH2 · Amino group · ion · 8 copies · chains I, J, K, M, O, P
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, N, B, I, J, C, E, D, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.61 | 0.76 | 52 | empty |
| 2 | 311 | 0.58 | 0.76 | 54 | empty |
| 3 | 180 | 0.51 | 0.78 | 26 | empty |
| 4 | 227 | 0.50 | 0.75 | 41 | empty |
| 5 | 149 | 0.49 | 0.78 | 29 | empty |
Interfaces
43 interfaces between chains.
- C–J · 828 Ų buried · 8 hydrogen bonds · protein-protein
- E–M · 821 Ų buried · 8 hydrogen bonds · protein-protein
- D–K · 818 Ų buried · 5 hydrogen bonds · protein-protein
- H–P · 813 Ų buried · 4 hydrogen bonds · protein-protein
- A–N · 811 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified, 16 disulfide, 8 covalent (nonstandard, disulfide, covalent ligand).
Compared structures
- 7TA6 · Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural… · the same entry in another collection · chain N against N, 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 P01375
- Elsewhere: RCSB PDB 7TA6 · PDBe 7TA6 · UniProt P01375
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