Research workbench
Structure of recombinant alphaec domain from human fibrinogen-420
Analyse Structure of recombinant alphaec domain from human fibrinogen-420 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FZD
- Type
- protein
- Length
- 1,576 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen-420
- UniProt
- P02671
- Ligands
- NAG, MAN, NDG, CA
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Fibrinogen-420 | protein | 197 | 15% helix, 28% strand | P02671 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, C, D, E, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 12 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.84 | 0.85 | 111 | empty |
| 2 | 1127 | 0.83 | 0.84 | 127 | empty |
| 3 | 90 | 0.53 | 0.84 | 16 | empty |
| 4 | 259 | 0.53 | 0.76 | 44 | empty |
| 5 | 113 | 0.45 | 0.78 | 23 | empty |
Interfaces
10 interfaces between chains.
- E–G · 422 Ų buried · 7 hydrogen bonds · protein-protein
- F–H · 416 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 414 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 408 Ų buried · 6 hydrogen bonds · protein-protein
- E–H · 399 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
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
- Elsewhere: RCSB PDB 1FZD · PDBe 1FZD · UniProt P02671
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