Research workbench
Interaction of human S100A6 (C3S) with V domain of receptor for advanced glycation end products (rage)
Analyse Interaction of human S100A6 (C3S) with V domain of receptor for advanced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2M1K
- Type
- protein
- Length
- 380 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein S100-A6; Advanced glycosylation end product-specific receptor
- UniProt
- P06703, Q15109
- Pockets
- 8 · best druggability 0.71
Structure
solution nmr · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Protein S100-A6 | protein | 89 | 70% helix, 2% strand | P06703 |
| A, C | Advanced glycosylation end product-specific receptor | protein | 101 | 4% helix, 42% strand | Q15109 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.71 | 0.93 | 18 | empty |
| 2 | 97 | 0.69 | 0.92 | 18 | empty |
| 3 | 64 | 0.67 | 0.94 | 18 | empty |
| 4 | 427 | 0.63 | 0.77 | 56 | empty |
| 5 | 350 | 0.63 | 0.79 | 48 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1301 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 353 Ų buried · 8 hydrogen bonds · protein-protein
- D–C · 343 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 138 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 125 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2M1K · Interaction of Human S100A6 (C3S) with V domain of Receptor for Advanced Glycation End… · the same entry in another collection · chain B against B, TM-score 1.00
- P06703 · AlphaFold monomer V2.0 prediction for protein S100-A6 (P06703) · a predicted model of the same protein · chain B against A, TM-score 0.93
- Q15109 · AlphaFold monomer V2.0 prediction for advanced glycosylation end product-specific… · a predicted model of the same protein · chain A against A, TM-score 0.68
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 P06703
- Every structure of UniProt Q15109
- Elsewhere: RCSB PDB 2M1K · PDBe 2M1K · UniProt P06703 · UniProt Q15109
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