Research workbench
Structural and biochemical characterization of fibrinogen binding to clfa from staphylocccus aureus
Analyse Structural and biochemical characterization of fibrinogen binding to clfa from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VR3
- Type
- protein
- Length
- 643 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clumping factor a; Fibrinogen gamma-chain
- UniProt
- Q2G015, P02679
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clumping factor a | protein | 308 | 4% helix, 54% strand | Q2G015 |
| B | Clumping factor a | protein | 310 | 5% helix, 55% strand | Q2G015 |
| C | Fibrinogen gamma-chain | protein | 12 | 0% helix, 83% strand | P02679 |
| D | Fibrinogen gamma-chain | protein | 13 | 0% helix, 85% strand | P02679 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.68 | 0.78 | 74 | empty |
| 2 | 120 | 0.60 | 0.86 | 28 | empty |
| 3 | 183 | 0.60 | 0.82 | 31 | empty |
| 4 | 127 | 0.36 | 0.73 | 27 | empty |
| 5 | 50 | 0.31 | 0.77 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 930 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 909 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 508 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2VR3 · Structural and Biochemical Characterization of Fibrinogen binding to ClfA from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2G015 · AlphaFold monomer V2.0 prediction for clumping factor a (Q2G015) · 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 D against A, TM-score 0.47
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 Q2G015
- Every structure of UniProt P02679
- Elsewhere: RCSB PDB 2VR3 · PDBe 2VR3 · UniProt Q2G015 · UniProt P02679
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.