Research workbench
Crystal structure of fragment D of GAMMAE132A fibrinogen
Analyse Crystal structure of fragment D of GAMMAE132A fibrinogen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RF0
- Type
- protein
- Length
- 1,323 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
- 19 · best druggability 0.60
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 | 64 | 78% helix, 2% strand | P02671 |
| B | Fibrinogen beta chain | protein | 306 | 25% helix, 25% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 298 | 23% helix, 23% strand | P02679 |
| D | Fibrinogen ALPHA/ALPHA-E chain | protein | 56 | 64% helix, 2% strand | P02671 |
| E | Fibrinogen beta chain | protein | 300 | 23% helix, 26% strand | P02675 |
| F | Fibrinogen gamma chain | protein | 299 | 25% helix, 26% 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
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.60 | 0.83 | 26 | empty |
| 2 | 171 | 0.59 | 0.82 | 25 | empty |
| 3 | 331 | 0.58 | 0.76 | 41 | empty |
| 4 | 279 | 0.55 | 0.76 | 32 | empty |
| 5 | 277 | 0.54 | 0.76 | 23 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2201 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2081 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1904 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1800 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 878 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1RF0 · Crystal Structure of Fragment D of gammaE132A 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 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 A against A, TM-score 0.88
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 1RF0 · PDBe 1RF0 · UniProt P02671 · UniProt P02675 · UniProt P02679
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