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Crystal structure analysis of S.EPIDERMIDIS adhesin sdrg binding to fibrinogen (apo structure)
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
- 1R19
- Type
- protein
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen-binding protein sdrg
- UniProt
- Q9KI13
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen-binding protein sdrg | protein | 286 | 4% helix, 50% strand | Q9KI13 |
| B | Fibrinogen-binding protein sdrg | protein | 300 | 3% helix, 53% strand | Q9KI13 |
| C | Fibrinogen-binding protein sdrg | protein | 298 | 4% helix, 50% strand | Q9KI13 |
| D | Fibrinogen-binding protein sdrg | protein | 292 | 3% helix, 52% strand | Q9KI13 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.72 | 0.78 | 106 | empty |
| 2 | 744 | 0.70 | 0.77 | 77 | empty |
| 3 | 197 | 0.68 | 0.86 | 35 | empty |
| 4 | 173 | 0.67 | 0.87 | 31 | empty |
| 5 | 502 | 0.64 | 0.76 | 61 | empty |
Interfaces
2 interfaces between chains.
- A–D · 534 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 461 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1R19 · Crystal Structure Analysis of S.epidermidis adhesin SdrG binding to Fibrinogen (Apo… · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.97
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 1R19 · PDBe 1R19 · UniProt Q9KI13
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