Research workbench
Crystal structure of recombinant GAMMAD364A fibrinogen fragment D with the peptide ligand gly-pro-arg-pro-amide
Analyse Crystal structure of recombinant GAMMAD364A fibrinogen fragment D with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BVH
- Type
- protein
- Length
- 1,322 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen gamma chain; 4-mer peptide gprp
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, FUC, CA
- Pockets
- 15 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibrinogen alpha chain | protein | 62 | 71% helix, 2% strand | P02671 |
| B, E | Fibrinogen beta chain | protein | 298 | 26% helix, 27% strand | P02675 |
| C, F | Fibrinogen gamma chain | protein | 293 | 23% helix, 26% strand | P02679 |
| G, I, H, J | 4-mer peptide gprp | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, J, E, H
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, 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
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.63 | 0.85 | 25 | empty |
| 2 | 201 | 0.58 | 0.81 | 34 | empty |
| 3 | 313 | 0.58 | 0.77 | 35 | empty |
| 4 | 161 | 0.58 | 0.82 | 25 | empty |
| 5 | 184 | 0.57 | 0.81 | 33 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2081 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2080 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1849 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1847 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 816 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3BVH · Crystal Structure of Recombinant gammaD364A Fibrinogen Fragment D 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 B 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 3BVH · PDBe 3BVH · UniProt P02671 · UniProt P02675 · UniProt P02679
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