Research workbench
Crystal structure analysis of S.EPIDERMIDIS adhesin sdrg binding to fibrinogen (adhesin-ligand complex)
Analyse Crystal structure analysis of S.EPIDERMIDIS adhesin sdrg binding to fibrinogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R17
- Type
- protein
- Length
- 663 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen-binding protein sdrg; Fibrinopeptide B
- UniProt
- Q9KI13
- Ligands
- CA
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen-binding protein sdrg | protein | 321 | 5% helix, 53% strand | Q9KI13 |
| B | Fibrinogen-binding protein sdrg | protein | 320 | 5% helix, 53% strand | Q9KI13 |
| C, D | Fibrinopeptide B | protein | 11 | 0% helix, 64% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.70 | 0.77 | 71 | empty |
| 2 | 241 | 0.54 | 0.77 | 38 | empty |
| 3 | 174 | 0.46 | 0.76 | 28 | empty |
| 4 | 105 | 0.44 | 0.78 | 22 | empty |
| 5 | 69 | 0.42 | 0.80 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–C · 944 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 928 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 921 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1R17 · Crystal Structure Analysis of S.epidermidis adhesin SdrG binding to Fibrinogen… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KI13 · AlphaFold monomer V2.0 prediction for serine-aspartate repeat- containing protein G… · a predicted model of the same protein · chain B against A, 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 Q9KI13
- Elsewhere: RCSB PDB 1R17 · PDBe 1R17 · UniProt Q9KI13
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.