MolNFT v1 · #7184 · protein
Crystal structure of fibrinogen fragment D
1FZA: “Crystal structure of fibrinogen fragment D”. X-ray diffraction, 2 ligands (NAG, CA), 16 pockets (best druggability 0.64). MolNFT v1 #7184 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FZA
- Type
- protein
- Length
- 1,414 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, CA
- Pockets
- 16 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibrinogen | protein | 85 | 71% helix, 1% strand | P02671 |
| B, E | Fibrinogen | protein | 313 | 22% helix, 21% strand | P02675 |
| C, F | Fibrinogen | protein | 309 | 26% helix, 25% strand | P02679 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
- CA · Calcium ion · metal · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.64 | 0.84 | 28 | empty |
| 2 | 213 | 0.64 | 0.83 | 26 | empty |
| 3 | 268 | 0.54 | 0.76 | 31 | empty |
| 4 | 108 | 0.54 | 0.83 | 26 | empty |
| 5 | 264 | 0.54 | 0.76 | 38 | empty |
Interfaces
8 interfaces between chains.
- E–F · 2291 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2287 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2193 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2188 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1080 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1FZA · Crystal structure of fibrinogen fragment D · 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 E 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 0.97
- P02671 · AlphaFold monomer V2.0 prediction for fibrinogen alpha chain (P02671) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 1FZA · PDBe 1FZA · UniProt P02671 · UniProt P02675 · UniProt P02679
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.