MolNFT v1 · #47435 · protein
Crystal structure of fragment D of GAMMAD298,301A fibrinogen with the peptide ligand gly-his-arg-pro-amide
2OYH · Fibrinogen alpha chain: “Crystal structure of fragment D of GAMMAD298,301A fibrinogen with the peptide ligand gly-his-arg-pro-amide”. X-ray diffraction, 3 ligands (NAG, FUC, CA), 16 pockets (best druggability 0.60). MolNFT v1 #47435…
- PDB
- 2OYH
- Type
- protein
- Length
- 1,311 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; Ghrp peptide
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, FUC, CA
- Pockets
- 16 · 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 chain | protein | 64 | 72% helix, 2% strand | P02671 |
| B | Fibrinogen beta chain | protein | 298 | 23% helix, 26% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 299 | 23% helix, 25% strand | P02679 |
| D | Fibrinogen alpha chain | protein | 54 | 59% helix, 2% strand | P02671 |
| E | Fibrinogen beta chain | protein | 295 | 24% helix, 27% strand | P02675 |
| F | Fibrinogen gamma chain | protein | 285 | 21% 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
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.60 | 0.83 | 25 | empty |
| 2 | 221 | 0.60 | 0.81 | 34 | empty |
| 3 | 133 | 0.59 | 0.85 | 26 | empty |
| 4 | 305 | 0.59 | 0.77 | 36 | empty |
| 5 | 159 | 0.58 | 0.82 | 28 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2137 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1905 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1819 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1612 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2OYH · Crystal Structure of Fragment D of gammaD298,301A 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 2OYH · PDBe 2OYH · UniProt P02671 · UniProt P02675 · UniProt P02679
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