MolNFT v1 · #110009 · protein

Crystal structure of MN(II) CA(II) NA(I) bound calprotectin

4XJK · Protein S100-A8: “Crystal structure of MN(II) CA(II) NA(I) bound calprotectin”. X-ray diffraction, 3 ligands (CA, NA, MN), 15 pockets (best druggability 0.83). MolNFT v1 #110009 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4XJK
Type: protein
Length: 984 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-A8; Protein S100-A9
UniProt: P05109, P06702
Ligands: CA, NA, MN
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 61% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, I	Protein S100-A8	protein	88	66% helix, 2% strand	P05109
B, F, J	Protein S100-A9	protein	108	57% helix, 4% strand	P06702
C, E	Protein S100-A8	protein	89	65% helix, 2% strand	P05109
D, H	Protein S100-A9	protein	109	57% helix, 3% strand	P06702

Ligands and binding sites

CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1045	0.83	0.83	69	empty
2	231	0.81	0.94	21	empty
3	820	0.77	0.81	61	empty
4	916	0.74	0.78	68	empty
5	838	0.72	0.77	64	empty

Interfaces

19 interfaces between chains.

G–H · 1643 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1630 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1627 Å² buried · 18 hydrogen bonds · protein-protein
I–J · 1619 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1600 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

4XJK · Crystal structure of Mn(II) Ca(II) Na(I) bound calprotectin · the same entry in another collection · chain J against J, TM-score 1.00
P06702 · AlphaFold monomer V2.0 prediction for protein S100-A9 (P06702) · a predicted model of the same protein · chain B 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 P05109
Every structure of UniProt P06702
Elsewhere: RCSB PDB 4XJK · PDBe 4XJK · UniProt P05109 · UniProt P06702

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.