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Asymmetric mtnf-alpha HTNFR1 complex

Analyse Asymmetric mtnf-alpha HTNFR1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KP8
Type: protein
Length: 673 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor; Tumor necrosis factor receptor superfamily member 1A
UniProt: P06804, P19438
Ligands: A7G
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 2% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor	protein	140	2% helix, 54% strand	P06804
B	Tumor necrosis factor	protein	140	2% helix, 54% strand	P06804
C	Tumor necrosis factor	protein	137	2% helix, 55% strand	P06804
E	Tumor necrosis factor receptor superfamily member 1A	protein	130	2% helix, 38% strand	P19438
F	Tumor necrosis factor receptor superfamily member 1A	protein	126	2% helix, 37% strand	P19438

Ligands and binding sites

A7G · 1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole · ligand · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	346	0.77	0.87	44	A7G
2	637	0.74	0.80	63	empty
3	404	0.69	0.81	55	empty
4	333	0.66	0.81	54	empty
5	213	0.54	0.78	33	empty

Interfaces

7 interfaces between chains.

B–C · 970 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 854 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 735 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 689 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 555 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 disulfide (disulfide).

Compared structures

7KP8 · asymmetric mTNF-alpha hTNFR1 complex · the same entry in another collection · chain F against F, TM-score 1.00
P06804 · AlphaFold monomer V2.0 prediction for tumor necrosis factor (P06804) · a predicted model of the same protein · chain B against A, TM-score 0.98
P19438 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain F against A, TM-score 0.96

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 P06804
Every structure of UniProt P19438
Elsewhere: RCSB PDB 7KP8 · PDBe 7KP8 · UniProt P06804 · UniProt P19438

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