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Structure of TNF receptor associated factor 2 in complex with a 5- residue CD40 peptide
Analyse Structure of TNF receptor associated factor 2 in complex with a 5- residue CD40… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D00
- Type
- protein
- Length
- 1,384 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor associated protein 2; B-cell surface antigen CD40
- UniProt
- P25942
- Ligands
- ACE, NH2
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Tumor necrosis factor receptor associated protein 2 | protein | 168 | 17% helix, 33% strand | — |
| I, J, K, L, M, N, O, P | B-cell surface antigen CD40 | protein | 5 | 0% helix, 40% strand | P25942 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 8 copies · chains A, I, B, F, J, C, K, D, H, L, E, M, N, G, O, P
- NH2 · Amino group · ion · 8 copies · chains A, I, B, J, K, L, E, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.75 | 0.78 | 74 | empty |
| 2 | 792 | 0.73 | 0.78 | 55 | empty |
| 3 | 475 | 0.61 | 0.75 | 37 | empty |
| 4 | 476 | 0.61 | 0.75 | 49 | empty |
| 5 | 456 | 0.59 | 0.74 | 54 | empty |
Interfaces
19 interfaces between chains.
- C–E · 600 Ų buried · 6 hydrogen bonds · protein-protein
- F–H · 592 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 590 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 580 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 556 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 1D00 · Structure of TNF receptor associated factor 2 in complex with a 5-residue CD40 peptide · the same entry in another collection · chain P against P, 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 P25942
- Elsewhere: RCSB PDB 1D00 · PDBe 1D00 · UniProt P25942
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