MolNFT v1 · #121120 · protein

Crystal structure of calcium and zinc-bound human S100A8 in space group P212121

5HLV · Protein S100-A8: “Crystal structure of calcium and zinc-bound human S100A8 in space group P212121”. X-ray diffraction, 3 ligands (CA, ZN, CL), 7 pockets (best druggability 0.85). MolNFT v1 #121120 on GenesisL1: 3D structure, binding…

PDB: 5HLV
Type: protein
Length: 710 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-A8
UniProt: P05109
Ligands: CA, ZN, CL
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, H	Protein S100-A8	protein	89	66% helix, 2% strand	P05109
C	Protein S100-A8	protein	88	67% helix, 2% strand	P05109
E, F	Protein S100-A8	protein	88	67% helix, 2% strand	P05109
G	Protein S100-A8	protein	90	66% helix, 2% strand	P05109

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
ZN · Zinc ion · metal · 8 copies · chains A, D, B, H, C, E, F, G
CL · Chloride ion · ion · 2 copies · chains F, G, B, H
ACT · Acetate ion · additive · 6 copies · chains A, C, E, B, F, G, D, H

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	921	0.85	0.86	84	ACT
2	602	0.84	0.89	74	ACT, CL
3	318	0.58	0.77	42	empty
4	110	0.39	0.75	20	empty
5	55	0.32	0.76	13	empty

Interfaces

18 interfaces between chains.

B–H · 1405 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 1394 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 1341 Å² buried · 13 hydrogen bonds · protein-protein
F–G · 1290 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 449 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5HLV · Crystal structure of calcium and zinc-bound human S100A8 in space group P212121 · the same entry in another collection · chain H against H, TM-score 1.00
P05109 · AlphaFold monomer V2.0 prediction for protein S100-A8 (P05109) · a predicted model of the same protein · chain E against A, TM-score 0.94

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
Elsewhere: RCSB PDB 5HLV · PDBe 5HLV · UniProt P05109

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