Research workbench

S100A12 complex with zinc in the absence of calcium

Analyse S100A12 complex with zinc in the absence of calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WC8
Type: protein
Length: 364 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-A12
UniProt: P80511
Ligands: NA, ZN
Pockets: 2 · best druggability 0.74

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein S100-A12	protein	88	69% helix, 5% strand	P80511
B	Protein S100-A12	protein	92	62% helix, 4% strand	P80511
C	Protein S100-A12	protein	91	67% helix, 4% strand	P80511
D	Protein S100-A12	protein	93	65% helix, 4% strand	P80511

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, C, B, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
CIT · Citric acid · additive · chains C, D

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

Pockets

2 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	847	0.74	0.78	89	empty
2	123	0.46	0.78	24	empty

Interfaces

6 interfaces between chains.

C–D · 1546 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1533 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 487 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 217 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 206 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2WC8 · S100A12 complex with zinc in the absence of calcium · the same entry in another collection · chain D against D, TM-score 1.00
P80511 · AlphaFold monomer V2.0 prediction for protein S100-A12 (P80511) · a predicted model of the same protein · chain A against A, TM-score 0.77

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 2WC8 · PDBe 2WC8 · UniProt P80511

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