MolNFT v1 · #162894 · protein

Crystal structure of human ngr-TNF

6RMJ · Tumor necrosis factor: “Crystal structure of human ngr-TNF”. X-ray diffraction, 4 pockets (best druggability 0.79). MolNFT v1 #162894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RMJ
Type: protein
Length: 436 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor
UniProt: P01375
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor	protein	149	2% helix, 50% strand	P01375
B	Tumor necrosis factor	protein	147	2% helix, 50% strand	P01375
C	Tumor necrosis factor	protein	140	2% helix, 51% strand	P01375

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	248	0.79	0.92	41	empty
2	70	0.76	0.99	17	empty
3	75	0.53	0.85	19	empty
4	62	0.27	0.72	16	empty

Interfaces

3 interfaces between chains.

A–B · 1287 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 1237 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1056 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6RMJ · Crystal structure of human NGR-TNF · the same entry in another collection · chain A against A, 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 6RMJ · PDBe 6RMJ · UniProt P01375

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