MolNFT v1 · #16927 · protein

The crystal structure of human S100A12 - copper complex

1ODB · Calgranulin C: “The crystal structure of human S100A12 - copper complex”. X-ray diffraction, 2 ligands (CA, CU), 4 pockets (best druggability 0.67). MolNFT v1 #16927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ODB
Type: protein
Length: 545 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calgranulin C
UniProt: P80511
Ligands: CA, CU
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Calgranulin C	protein	91	65% helix, 2% strand	P80511
F	Calgranulin C	protein	90	64% helix, 2% strand	P80511

Ligands and binding sites

CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

4 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	698	0.67	0.76	69	empty
2	83	0.38	0.77	12	empty
3	77	0.35	0.76	14	empty
4	54	0.31	0.77	11	empty

Interfaces

9 interfaces between chains.

E–F · 1563 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1549 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1480 Å² buried · 16 hydrogen bonds · protein-protein
C–E · 517 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 427 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1ODB · The crystal structure of human S100A12 - copper complex · 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 A against A, TM-score 0.98

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 1ODB · PDBe 1ODB · UniProt P80511

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