MolNFT v1 · #15551 · protein
Crystal structure of human D-dimer from cross-linked fibrin complexed with gpr and ghrpldk peptide ligands.
1N86 · Fibrin ALPHA/ALPHA-E chain: “Crystal structure of human D-dimer from cross-linked fibrin complexed with gpr and ghrpldk peptide ligands.”. X-ray diffraction, 3 ligands (NDG, MAN, CA), 19 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 1N86
- Type
- protein
- Length
- 1,366 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrin ALPHA/ALPHA-E chain; Fibrin beta chain; Fibrin gamma chain; Fibrin alpha chain…
- UniProt
- P02671, P02675
- Ligands
- NDG, MAN, CA
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibrin ALPHA/ALPHA-E chain | protein | 74 | 58% helix, 0% strand | P02671 |
| B, E | Fibrin beta chain | protein | 307 | 25% helix, 24% strand | P02675 |
| C, F | Fibrin gamma chain | protein | 295 | 23% helix, 26% strand | — |
| G, H | Fibrin alpha chain peptide ligand fragment gly-pro-arg | protein | 3 | 0% helix, 0% strand | P02671 |
| I, J | Fibrin beta chain peptide ligand fragment gly-his-arg-pro- leu-asp-lys | protein | 4 | 0% helix, 0% strand | P02675 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains B, I, E, J
- MAN · alpha-D-mannopyranose · sugar
- 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
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.71 | 0.81 | 53 | empty |
| 2 | 249 | 0.62 | 0.80 | 32 | empty |
| 3 | 339 | 0.58 | 0.76 | 46 | empty |
| 4 | 124 | 0.55 | 0.83 | 26 | empty |
| 5 | 248 | 0.55 | 0.77 | 33 | empty |
Interfaces
11 interfaces between chains.
- B–C · 2231 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2189 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1981 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1935 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 887 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1N86 · Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and… · the same entry in another collection · chain J against J, TM-score 1.00
- P02671 · AlphaFold monomer V2.0 prediction for fibrinogen alpha chain (P02671) · a predicted model of the same protein · chain G against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 1N86 · PDBe 1N86 · UniProt P02671 · UniProt P02675
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