MolNFT v1 · #13955 · protein
Crystal structure of recombinant human fibrinogen fragment D
1LT9 · Fibrinogen ALPHA/ALPHA-E chain: “Crystal structure of recombinant human fibrinogen fragment D”. X-ray diffraction, 2 ligands (NAG, CA), 18 pockets (best druggability 0.60). MolNFT v1 #13955 on GenesisL1: 3D structure, binding sites…
- PDB
- 1LT9
- Type
- protein
- Length
- 1,299 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen ALPHA/ALPHA-E chain; Fibrinogen beta chain; Fibrinogen gamma chain
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, CA
- Pockets
- 18 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen ALPHA/ALPHA-E chain | protein | 65 | 78% helix, 2% strand | P02671 |
| B | Fibrinogen beta chain | protein | 298 | 21% helix, 25% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 299 | 21% helix, 25% strand | P02679 |
| D | Fibrinogen ALPHA/ALPHA-E chain | protein | 58 | 62% helix, 2% strand | P02671 |
| E | Fibrinogen beta chain | protein | 294 | 22% helix, 26% strand | P02675 |
| F | Fibrinogen gamma chain | protein | 285 | 22% helix, 28% strand | P02679 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
- CA · Calcium ion · metal · 6 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.60 | 0.83 | 25 | empty |
| 2 | 154 | 0.58 | 0.83 | 24 | empty |
| 3 | 308 | 0.58 | 0.77 | 35 | empty |
| 4 | 313 | 0.57 | 0.76 | 36 | empty |
| 5 | 198 | 0.52 | 0.77 | 19 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2231 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1974 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1929 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1707 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 919 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1LT9 · Crystal Structure of Recombinant Human Fibrinogen Fragment D · the same entry in another collection · chain A against A, 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
- P02679 · AlphaFold monomer V2.0 prediction for fibrinogen gamma chain (P02679) · a predicted model of the same protein · chain F against A, TM-score 0.99
- P02671 · AlphaFold monomer V2.0 prediction for fibrinogen alpha chain (P02671) · a predicted model of the same protein · chain D against A, TM-score 0.87
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 1LT9 · PDBe 1LT9 · UniProt P02671 · UniProt P02675 · UniProt P02679
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