Research workbench
Fragment double-D from human fibrin
Analyse Fragment double-D from human fibrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N8E
- Type
- protein
- Length
- 1,352 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrin ALPHA/ALPHA-E chain; Fibrin beta chain; Fibrin gamma chain
- UniProt
- P02671, P02675, P02679
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibrin ALPHA/ALPHA-E chain | protein | 74 | 0% helix, 0% strand | P02671 |
| B, E | Fibrin beta chain | protein | 307 | 0% helix, 0% strand | P02675 |
| C, F | Fibrin gamma chain | protein | 295 | 0% helix, 0% strand | P02679 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.40 | 0.73 | 34 | empty |
| 2 | 74 | 0.32 | 0.72 | 27 | empty |
| 3 | 58 | 0.29 | 0.72 | 16 | empty |
Interfaces
7 interfaces between chains.
- E–F · 241 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 223 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 190 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1N8E · Fragment Double-D from Human Fibrin · the same entry in another collection · chain F against F, 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 0.98
- P02679 · AlphaFold monomer V2.0 prediction for fibrinogen gamma chain (P02679) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P02671 · AlphaFold monomer V2.0 prediction for fibrinogen alpha chain (P02671) · a predicted model of the same protein · chain A against A, TM-score 0.87
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
- Elsewhere: RCSB PDB 1N8E · PDBe 1N8E · UniProt P02671 · UniProt P02675 · UniProt P02679
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