MolNFT v1 · #124203 · protein

Crystal structure of human calcium-bound S100A1

5K89 · Protein S100-A1: “Crystal structure of human calcium-bound S100A1”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.52). MolNFT v1 #124203 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K89
Type: protein
Length: 263 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-A1
UniProt: P23297
Ligands: CA
Pockets: 8 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 64% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein S100-A1	protein	85	65% helix, 5% strand	P23297
C	Protein S100-A1	protein	89	63% helix, 2% strand	P23297
H	Protein S100-A1	protein	89	64% helix, 4% strand	P23297

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, C, H
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	212	0.52	0.76	33	empty
2	93	0.44	0.78	15	empty
3	72	0.41	0.79	17	empty
4	77	0.41	0.79	18	empty
5	63	0.32	0.76	12	empty

Interfaces

3 interfaces between chains.

A–H · 441 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 376 Å² buried · 4 hydrogen bonds · protein-protein
C–H · 267 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5K89 · Crystal Structure of Human Calcium-Bound S100A1 · the same entry in another collection · chain A against A, TM-score 1.00
P23297 · AlphaFold monomer V2.0 prediction for protein S100-A1 (P23297) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P23297
Elsewhere: RCSB PDB 5K89 · PDBe 5K89 · UniProt P23297

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