Research workbench
A fragment of streptococcal M1 protein in complex with human fibrinogen
Analyse A fragment of streptococcal M1 protein in complex with human fibrinogen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XNY
- Type
- protein
- Length
- 1,359 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 7.5
- Source
- HOMO SAPIENS; STREPTOCOCCUS PYOGENES
- Molecule
- Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen gamma chain; M protein
- UniProt
- P02671, P02675, P02679, Q48WD8
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · resolution 7.5 · 5 distinct chains · 23% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibrinogen alpha chain | protein | 57 | 51% helix, 2% strand | P02671 |
| B, E | Fibrinogen beta chain | protein | 298 | 20% helix, 27% strand | P02675 |
| C, F | Fibrinogen gamma chain | protein | 288 | 22% helix, 25% strand | P02679 |
| M | M protein | protein | 37 | 8% helix, 0% strand | Q48WD8 |
| N | M protein | protein | 36 | 22% helix, 0% strand | Q48WD8 |
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 | 324 | 0.67 | 0.81 | 35 | empty |
| 2 | 126 | 0.60 | 0.85 | 31 | empty |
| 3 | 189 | 0.60 | 0.82 | 26 | empty |
| 4 | 174 | 0.59 | 0.82 | 25 | empty |
| 5 | 290 | 0.57 | 0.77 | 37 | empty |
Interfaces
15 interfaces between chains.
- B–C · 1942 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1937 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1804 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1800 Ų buried · 22 hydrogen bonds · protein-protein
- M–N · 948 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 isopeptide (disulfide, isopeptide).
Compared structures
- 2XNY · A fragment of streptococcal M1 protein in complex with human fibrinogen · the same entry in another collection · chain N against N, TM-score 1.00
- P02675 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (P02675) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P02679 · AlphaFold monomer V2.0 prediction for fibrinogen gamma chain (P02679) · a predicted model of the same protein · chain F 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 P02671
- Every structure of UniProt P02675
- Every structure of UniProt P02679
- Every structure of UniProt Q48WD8
- Elsewhere: RCSB PDB 2XNY · PDBe 2XNY · UniProt P02671 · UniProt P02675 · UniProt P02679 · UniProt Q48WD8
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