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Human TNF-alpha in complex with JNJ525

Analyse Human TNF-alpha in complex with JNJ525 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MU8
Type: protein
Length: 6,955 residues
Chains: 48
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor
UniProt: P01375
Ligands: JNI
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 24 distinct chains · 2% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor	protein	141	2% helix, 49% strand	P01375
B	Tumor necrosis factor	protein	145	2% helix, 48% strand	P01375
C, T	Tumor necrosis factor	protein	146	2% helix, 51% strand	P01375
D, G, K, M, Q, S, U, Y, a, e, q, s	Tumor necrosis factor	protein	149	0% helix, 49% strand	P01375
F	Tumor necrosis factor	protein	140	2% helix, 51% strand	P01375
H, X, j	Tumor necrosis factor	protein	150	2% helix, 50% strand	P01375
I	Tumor necrosis factor	protein	141	2% helix, 53% strand	P01375
J, V, d	Tumor necrosis factor	protein	138	0% helix, 50% strand	P01375
L	Tumor necrosis factor	protein	142	2% helix, 51% strand	P01375
N, Z, l, t	Tumor necrosis factor	protein	143	2% helix, 48% strand	P01375
O, c	Tumor necrosis factor	protein	145	2% helix, 50% strand	P01375
P	Tumor necrosis factor	protein	145	2% helix, 50% strand	P01375
R	Tumor necrosis factor	protein	138	2% helix, 53% strand	P01375
W	Tumor necrosis factor	protein	143	2% helix, 51% strand	P01375
b	Tumor necrosis factor	protein	144	2% helix, 49% strand	P01375
f	Tumor necrosis factor	protein	143	2% helix, 48% strand	P01375
g, i, u, w	Tumor necrosis factor	protein	145	2% helix, 50% strand	P01375
h	Tumor necrosis factor	protein	137	2% helix, 50% strand	P01375
k	Tumor necrosis factor	protein	142	2% helix, 53% strand	P01375
m	Tumor necrosis factor	protein	147	2% helix, 50% strand	P01375
n	Tumor necrosis factor	protein	147	2% helix, 46% strand	P01375
o	Tumor necrosis factor	protein	147	0% helix, 49% strand	P01375
p	Tumor necrosis factor	protein	139	2% helix, 50% strand	P01375
r, v	Tumor necrosis factor	protein	144	2% helix, 44% strand	P01375

Ligands and binding sites

JNI · ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine · ligand · 46 copies · chains A, B, D, C, F, G, I, H, J, K, L, M, N, O, P, Q, R, S, U, T, V, W, Y, X, Z, a, c, b, d, e, g, f, h, i, k, j, l, m, o, n, p, q, s, r, t, u, w, v

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	977	0.87	0.88	124	empty
2	1086	0.85	0.86	124	empty
3	937	0.79	0.81	101	empty
4	523	0.78	0.84	63	empty
5	496	0.77	0.84	69	empty

Interfaces

104 interfaces between chains.

d–e · 1230 Å² buried · 11 hydrogen bonds · protein-protein
p–q · 1211 Å² buried · 12 hydrogen bonds · protein-protein
V–W · 1183 Å² buried · 11 hydrogen bonds · protein-protein
J–K · 1169 Å² buried · 10 hydrogen bonds · protein-protein
T–U · 1169 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide (disulfide).

Compared structures

5MU8 · Human TNF-alpha in complex with JNJ525 · the same entry in another collection · chain B against B, 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 5MU8 · PDBe 5MU8 · UniProt P01375

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