MolNFT v1 · #107003 · protein

Human tnfa dimer in complex with the semi-synthetic bicyclic peptide M21

4TWT · Tumor necrosis factor: “Human tnfa dimer in complex with the semi-synthetic bicyclic peptide M21”. X-ray diffraction, 1 ligand (38A), 8 pockets (best druggability 0.62). MolNFT v1 #107003 on GenesisL1: 3D structure, binding sites…

PDB: 4TWT
Type: protein
Length: 587 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor; Ala-cys-pro-pro-cys-leu-TRP-gln-val-leu-cys-gly
UniProt: P01375
Ligands: 38A
Pockets: 8 · best druggability 0.62

Structure

x-ray diffraction · 5 distinct chains · 3% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor	protein	150	2% helix, 49% strand	P01375
B	Tumor necrosis factor	protein	139	2% helix, 51% strand	P01375
E, F	Ala-cys-pro-pro-cys-leu-TRP-gln-val-leu-cys-gly	protein	12	33% helix, 0% strand	—
C	Tumor necrosis factor	protein	143	2% helix, 50% strand	P01375
D	Tumor necrosis factor	protein	131	2% helix, 52% strand	P01375

Ligands and binding sites

38A · (2,4,6-trimethylbenzene-1,3,5-triyl)trimethanol · ligand · 2 copies · chains B, E, F, D
GOL · Glycerol · additive · 6 copies · chains A, B, E, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	150	0.62	0.85	25	empty
2	353	0.61	0.77	39	empty
3	119	0.55	0.83	22	GOL
4	169	0.53	0.79	33	GOL
5	91	0.48	0.81	19	empty

Interfaces

9 interfaces between chains.

A–B · 1149 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 989 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 409 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 396 Å² buried · 4 hydrogen bonds · protein-protein
F–D · 391 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent, 4 disulfide (covalent ligand, disulfide).

Compared structures

4TWT · Human TNFa dimer in complex with the semi-synthetic bicyclic peptide M21 · 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 4TWT · PDBe 4TWT · UniProt P01375

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