MolNFT v1 · #146782 · protein

Crystal structure of NI(II)-bound human calprotectin

6DS2 · Protein S100-A8: “Crystal structure of NI(II)-bound human calprotectin”. X-ray diffraction, 2 ligands (NA, NI), 11 pockets (best druggability 0.83). MolNFT v1 #146782 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DS2
Type: protein
Length: 788 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-A8; Protein S100-A9
UniProt: P05109, P06702
Ligands: NA, NI
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 61% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Protein S100-A8	protein	89	66% helix, 2% strand	P05109
B, F	Protein S100-A9	protein	108	57% helix, 4% strand	P06702
D	Protein S100-A9	protein	108	57% helix, 4% strand	P06702
G	Protein S100-A8	protein	88	67% helix, 2% strand	P05109
H	Protein S100-A9	protein	109	60% helix, 4% strand	P06702

Ligands and binding sites

NA · Sodium ion · metal · 10 copies · chains A, C, D, E, F, G
NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F, G, H

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

Pockets

11 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	1180	0.83	0.84	88	empty
2	193	0.81	0.95	22	empty
3	770	0.76	0.81	64	empty
4	909	0.71	0.76	114	empty
5	50	0.37	0.80	13	empty

Interfaces

15 interfaces between chains.

G–H · 1628 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1626 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1610 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1605 Å² buried · 22 hydrogen bonds · protein-protein
F–H · 503 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6DS2 · Crystal structure of Ni(II)-bound human calprotectin · the same entry in another collection · chain H against H, TM-score 1.00
P06702 · AlphaFold monomer V2.0 prediction for protein S100-A9 (P06702) · a predicted model of the same protein · chain D against A, TM-score 0.96
P05109 · AlphaFold monomer V2.0 prediction for protein S100-A8 (P05109) · a predicted model of the same protein · chain G against A, TM-score 0.92

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 6DS2 · PDBe 6DS2 · UniProt P05109 · UniProt P06702

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