MolNFT v1 · #66592 · protein
Crystal structure of recombinant gamma N308K fibrinogen fragment D with the peptide ligand gly-pro-arg-pro-amide
3HUS · Fibrinogen alpha chain: “Crystal structure of recombinant gamma N308K fibrinogen fragment D with the peptide ligand…”. X-ray diffraction, 3 ligands (NAG, FUC, CA), 13 pockets (best druggability 0.60). MolNFT v1 #66592 on GenesisL1…
- PDB
- 3HUS
- Type
- protein
- Length
- 1,328 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; Peptide ligand…
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, FUC, CA
- Pockets
- 13 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibrinogen alpha chain | protein | 61 | 59% helix, 0% strand | P02671 |
| B, E | Fibrinogen beta chain | protein | 303 | 19% helix, 25% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 291 | 21% helix, 28% strand | P02679 |
| F | Fibrinogen gamma chain | protein | 293 | 19% helix, 24% strand | P02679 |
| G, H, I, J | Peptide ligand gly-pro-arg-pro-amide | 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, E
- 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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.60 | 0.83 | 28 | empty |
| 2 | 152 | 0.60 | 0.84 | 26 | empty |
| 3 | 190 | 0.56 | 0.80 | 33 | empty |
| 4 | 286 | 0.54 | 0.75 | 33 | empty |
| 5 | 231 | 0.53 | 0.77 | 25 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2109 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2084 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1909 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1860 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 788 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3HUS · Crystal structure of recombinant gamma N308K fibrinogen fragment D with the peptide… · 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 3HUS · PDBe 3HUS · UniProt P02671 · UniProt P02675 · UniProt P02679
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