MolNFT v1 · #137856 · protein

Crystal structure of NI(II)- and CA(II)-bound human calprotectin

5W1F · Protein S100-A8: “Crystal structure of NI(II)- and CA(II)-bound human calprotectin”. X-ray diffraction, 3 ligands (CA, NA, NI), 12 pockets (best druggability 0.83). MolNFT v1 #137856 on GenesisL1: 3D structure, binding sites and…

PDB: 5W1F
Type: protein
Length: 779 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: CA, NA, NI
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 61% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein S100-A8	protein	87	67% helix, 2% strand	P05109
B, H	Protein S100-A9	protein	107	58% helix, 2% strand	P06702
C, G, E	Protein S100-A8	protein	88	67% helix, 5% strand	P05109
D	Protein S100-A9	protein	108	56% helix, 2% strand	P06702
F	Protein S100-A9	protein	106	58% helix, 2% strand	P06702

Ligands and binding sites

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

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	1100	0.83	0.84	83	empty
2	245	0.83	0.95	23	empty
3	798	0.77	0.81	60	empty
4	459	0.66	0.78	47	empty
5	326	0.59	0.77	34	empty

Interfaces

15 interfaces between chains.

C–D · 1636 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1633 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1597 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1593 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 523 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5W1F · Crystal structure of Ni(II)- and Ca(II)-bound human calprotectin · the same entry in another collection · chain F against F, 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
P05109 · AlphaFold monomer V2.0 prediction for protein S100-A8 (P05109) · a predicted model of the same protein · chain C against A, TM-score 0.91

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 5W1F · PDBe 5W1F · UniProt P05109 · UniProt P06702

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