MolNFT v1 · #20416 · protein
Crystal structure of fragment D of BBETAD398A fibrinogen
1RE4 · Fibrinogen ALPHA/ALPHA-E chain: “Crystal structure of fragment D of BBETAD398A fibrinogen”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.63). MolNFT v1 #20416 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1RE4
- Type
- protein
- Length
- 1,314 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen ALPHA/ALPHA-E chain; Fibrinogen beta chain; Fibrinogen gamma chain
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen ALPHA/ALPHA-E chain | protein | 65 | 71% helix, 2% strand | P02671 |
| B | Fibrinogen beta chain | protein | 306 | 23% helix, 25% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 298 | 23% helix, 23% strand | P02679 |
| D | Fibrinogen ALPHA/ALPHA-E chain | protein | 60 | 62% helix, 2% strand | P02671 |
| E | Fibrinogen beta chain | protein | 294 | 23% helix, 26% strand | P02675 |
| F | Fibrinogen gamma chain | protein | 291 | 24% 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 · 6 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.63 | 0.84 | 27 | empty |
| 2 | 201 | 0.61 | 0.82 | 26 | empty |
| 3 | 341 | 0.59 | 0.77 | 40 | empty |
| 4 | 292 | 0.58 | 0.77 | 29 | empty |
| 5 | 274 | 0.56 | 0.77 | 22 | empty |
Interfaces
8 interfaces between chains.
- B–C · 2242 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1979 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1918 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1684 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 884 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1RE4 · Crystal Structure of Fragment D of BbetaD398A Fibrinogen · 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 0.99
- 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
- P02671 · AlphaFold monomer V2.0 prediction for fibrinogen alpha chain (P02671) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 1RE4 · PDBe 1RE4 · UniProt P02671 · UniProt P02675 · UniProt P02679
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.