Research workbench

Calcium-free (apo) S100A12

Analyse Calcium-free (apo) S100A12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WCF
Type: protein
Length: 538 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-A12
UniProt: P80511
Ligands: NA
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 66% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein S100-A12	protein	91	69% helix, 7% strand	P80511
C	Protein S100-A12	protein	90	67% helix, 4% strand	P80511
D	Protein S100-A12	protein	88	65% helix, 7% strand	P80511
E	Protein S100-A12	protein	90	66% helix, 4% strand	P80511
F	Protein S100-A12	protein	88	66% helix, 7% strand	P80511

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains B, E

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

Pockets

3 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	954	0.74	0.77	72	empty
2	197	0.56	0.79	27	empty
3	51	0.53	0.88	16	empty

Interfaces

11 interfaces between chains.

A–B · 1478 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1423 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1386 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 369 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 272 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2WCF · calcium-free (apo) S100A12 · the same entry in another collection · chain F against F, TM-score 1.00
P80511 · AlphaFold monomer V2.0 prediction for protein S100-A12 (P80511) · a predicted model of the same protein · chain F against A, TM-score 0.67

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 P80511
Elsewhere: RCSB PDB 2WCF · PDBe 2WCF · UniProt P80511

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