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Mtnf-alpha HTNFR1 complex

Analyse 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: 7KPB
Type: protein
Length: 1,141 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor; Tumor necrosis factor receptor superfamily member 1A; FAB1974…
UniProt: P01375, P19438
Ligands: D84, NAG
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 7 distinct chains · 3% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor	protein	153	2% helix, 50% strand	P01375
B	Tumor necrosis factor	protein	143	2% helix, 52% strand	P01375
C	Tumor necrosis factor	protein	138	2% helix, 50% strand	P01375
F	Tumor necrosis factor receptor superfamily member 1A	protein	141	2% helix, 39% strand	P19438
E	Tumor necrosis factor receptor superfamily member 1A	protein	141	2% helix, 40% strand	P19438
L	FAB1974 - light chain	protein	213	6% helix, 52% strand	—
H	FAB1974 - heavy chain	protein	212	6% helix, 49% strand	—

Ligands and binding sites

D84 · 5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one · ligand · chains A, B, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
GOL · Glycerol · additive · 9 copies · chains A, H, B, E, F, C, L

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

Pockets

17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	438	0.81	0.88	54	D84
2	966	0.75	0.78	105	GOL
3	71	0.73	0.97	26	empty
4	71	0.73	0.97	26	empty
5	279	0.65	0.82	64	empty

Interfaces

12 interfaces between chains.

L–H · 1608 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1155 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1030 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 907 Å² buried · 17 hydrogen bonds · protein-protein
B–F · 865 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7KPB · Human TNF-alpha TNFR1 complex bound to conformationally selective antibody · the same entry in another collection · chain H against H, TM-score 1.00
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 0.93

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
Every structure of UniProt P19438
Elsewhere: RCSB PDB 7KPB · PDBe 7KPB · UniProt P01375 · UniProt P19438

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