MolNFT v1 · #117850 · protein

Crystal structure of truncated CCL21

5EKI · C-C motif chemokine 21: “Crystal structure of truncated CCL21”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.53). MolNFT v1 #117850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EKI
Type: protein
Length: 427 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-C motif chemokine 21
UniProt: O00585
Ligands: SO4
Pockets: 12 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C-C motif chemokine 21	protein	72	18% helix, 25% strand	O00585
B, D	C-C motif chemokine 21	protein	71	18% helix, 28% strand	O00585
C, F	C-C motif chemokine 21	protein	70	23% helix, 26% strand	O00585
E	C-C motif chemokine 21	protein	73	18% helix, 25% strand	O00585

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, D, B, C, F, E

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	161	0.53	0.80	20	empty
2	145	0.52	0.80	28	empty
3	185	0.51	0.78	23	empty
4	147	0.51	0.79	23	empty
5	126	0.51	0.80	19	empty

Interfaces

6 interfaces between chains.

B–E · 817 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 771 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 753 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 703 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 699 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5EKI · Crystal Structure of Truncated CCL21 · the same entry in another collection · chain C against C, TM-score 1.00
O00585 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 21 (O00585) · a predicted model of the same protein · chain A 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 O00585
Elsewhere: RCSB PDB 5EKI · PDBe 5EKI · UniProt O00585

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