MolNFT v1 · #8096 · protein
The structure of S100A12 in a hexameric form and its proposed role in receptor signalling
1GQM · Calgranulin C: “The structure of S100A12 in a hexameric form and its proposed role in receptor signalling”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability 0.67). MolNFT v1 #8096 on GenesisL1: 3D structure, binding…
- PDB
- 1GQM
- Type
- protein
- Length
- 1,045 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calgranulin C
- UniProt
- P80511
- Ligands
- CA
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, I, J, K | Calgranulin C | protein | 87 | 64% helix, 5% strand | P80511 |
| B, H | Calgranulin C | protein | 88 | 65% helix, 2% strand | P80511 |
| L | Calgranulin C | protein | 86 | 64% helix, 2% strand | P80511 |
Ligands and binding sites
- CA · Calcium ion · metal · 36 copies · chains A, D, B, F, C, E, G, I, H, L, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.67 | 0.74 | 88 | empty |
| 2 | 605 | 0.63 | 0.74 | 62 | empty |
| 3 | 518 | 0.61 | 0.75 | 52 | empty |
| 4 | 464 | 0.61 | 0.75 | 38 | empty |
| 5 | 568 | 0.61 | 0.73 | 58 | empty |
Interfaces
28 interfaces between chains.
- A–B · 1466 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1428 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1412 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1397 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1385 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1GQM · The structure of S100A12 in a hexameric form and its proposed role in receptor signalling · the same entry in another collection · chain L against L, TM-score 1.00
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 1GQM · PDBe 1GQM · UniProt P80511
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