Research workbench
Crystal structure of fragment D of BBETAD398A fibrinogen with the peptide ligand gly-his-arg-pro-amide
Analyse Crystal structure of fragment D of BBETAD398A fibrinogen with the peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RE3
- Type
- protein
- Length
- 1,305 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen ALPHA/ALPHA-E chain; Fibrinogen beta chain; Fibrinogen gamma chain; Ghrp…
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, CA
- Pockets
- 15 · best druggability 0.60
Structure
x-ray diffraction · 7 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen ALPHA/ALPHA-E chain | protein | 60 | 60% helix, 2% strand | P02671 |
| B | Fibrinogen beta chain | protein | 294 | 20% helix, 27% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 288 | 23% helix, 26% strand | P02679 |
| D | Fibrinogen ALPHA/ALPHA-E chain | protein | 63 | 67% helix, 2% strand | P02671 |
| E | Fibrinogen beta chain | protein | 301 | 22% helix, 26% strand | P02675 |
| F | Fibrinogen gamma chain | protein | 291 | 24% helix, 24% strand | P02679 |
| G, H | Ghrp peptide | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, E
- CA · Calcium ion · metal · 5 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.60 | 0.83 | 26 | empty |
| 2 | 176 | 0.58 | 0.81 | 30 | empty |
| 3 | 264 | 0.57 | 0.77 | 36 | empty |
| 4 | 322 | 0.57 | 0.76 | 30 | empty |
| 5 | 126 | 0.53 | 0.82 | 22 | empty |
Interfaces
8 interfaces between chains.
- B–C · 2004 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1969 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1861 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1765 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 837 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1RE3 · Crystal Structure of Fragment D of BbetaD398A Fibrinogen with the Peptide Ligand… · the same entry in another collection · chain H against H, 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 0.99
- P02679 · AlphaFold monomer V2.0 prediction for fibrinogen gamma chain (P02679) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 1RE3 · PDBe 1RE3 · UniProt P02671 · UniProt P02675 · UniProt P02679
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