Research workbench
Crystal structure of fragment D of GAMMAE132A fibrinogen with the peptide ligand gly-his-arg-pro-amide
Analyse Crystal structure of fragment D of GAMMAE132A 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
- 1RF1
- Type
- protein
- Length
- 1,319 residues
- Chains
- 10
- 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, FUC, CA
- Pockets
- 14 · best druggability 0.60
Structure
x-ray diffraction · 7 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen ALPHA/ALPHA-E chain | protein | 64 | 66% helix, 2% strand | P02671 |
| B | Fibrinogen beta chain | protein | 299 | 24% helix, 27% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 298 | 24% helix, 26% strand | P02679 |
| D | Fibrinogen ALPHA/ALPHA-E chain | protein | 56 | 61% helix, 2% strand | P02671 |
| E | Fibrinogen beta chain | protein | 295 | 23% helix, 27% strand | P02675 |
| F | Fibrinogen gamma chain | protein | 291 | 23% helix, 26% strand | P02679 |
| G, H, I, J | 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, H, E, J
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, H, E, J
- CA · Calcium ion · metal · 4 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.60 | 0.83 | 26 | empty |
| 2 | 157 | 0.59 | 0.83 | 25 | empty |
| 3 | 288 | 0.58 | 0.77 | 32 | empty |
| 4 | 208 | 0.57 | 0.80 | 34 | empty |
| 5 | 221 | 0.56 | 0.79 | 34 | empty |
Interfaces
11 interfaces between chains.
- B–C · 2127 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1939 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1810 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1666 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 853 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1RF1 · Crystal Structure of Fragment D of gammaE132A Fibrinogen with the Peptide Ligand… · the same entry in another collection · chain J against J, 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
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 1RF1 · PDBe 1RF1 · UniProt P02671 · UniProt P02675 · UniProt P02679
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