MolNFT v1 · #16178 · protein

High resolution crystal structures of thymus and activation-regulated chemokine

1NR4: “High resolution crystal structures of thymus and activation-regulated chemokine”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.73). MolNFT v1 #16178 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NR4
Type: protein
Length: 524 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymus and activation-regulated chemokine
UniProt: Q92583
Ligands: SO4
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymus and activation-regulated chemokine	protein	67	22% helix, 28% strand	Q92583
B	Thymus and activation-regulated chemokine	protein	64	27% helix, 30% strand	Q92583
C	Thymus and activation-regulated chemokine	protein	66	23% helix, 32% strand	Q92583
D	Thymus and activation-regulated chemokine	protein	63	25% helix, 32% strand	Q92583
E	Thymus and activation-regulated chemokine	protein	69	25% helix, 28% strand	Q92583
F	Thymus and activation-regulated chemokine	protein	66	26% helix, 29% strand	Q92583
G	Thymus and activation-regulated chemokine	protein	66	23% helix, 27% strand	Q92583
H	Thymus and activation-regulated chemokine	protein	63	27% helix, 29% strand	Q92583

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	896	0.73	0.77	67	empty
2	158	0.52	0.79	23	SO4
3	111	0.42	0.76	25	empty
4	97	0.40	0.77	17	empty
5	81	0.35	0.76	20	empty

Interfaces

7 interfaces between chains.

E–F · 887 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 886 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 834 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 810 Å² buried · 16 hydrogen bonds · protein-protein
D–G · 350 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

1NR4 · High resolution crystal structures of thymus and activation-regulated chemokine · the same entry in another collection · chain G against G, TM-score 1.00
Q92583 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 17 (Q92583) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q92583
Elsewhere: RCSB PDB 1NR4 · PDBe 1NR4 · UniProt Q92583

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