Research workbench
Crystal structure of human fibrinogen
Analyse Crystal structure of human fibrinogen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GHG
- Type
- protein
- Length
- 3,892 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen gamma chain; A knob; B knob
- UniProt
- P02671, P02675, P02679
- Ligands
- NDG, MAN, NAG, GAL, SIA, BMA, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 9 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Fibrinogen alpha chain | protein | 174 | 71% helix, 3% strand | P02671 |
| B, E, H, K | Fibrinogen beta chain | protein | 401 | 37% helix, 19% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 381 | 36% helix, 20% strand | P02679 |
| F | Fibrinogen gamma chain | protein | 382 | 32% helix, 15% strand | P02679 |
| I | Fibrinogen gamma chain | protein | 394 | 35% helix, 18% strand | P02679 |
| J | Fibrinogen alpha chain | protein | 186 | 68% helix, 2% strand | P02671 |
| L | Fibrinogen gamma chain | protein | 391 | 37% helix, 21% strand | P02679 |
| M, N, Q, R | A knob | protein | 4 | 0% helix, 25% strand | — |
| O, P, S, T | B knob | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 10 copies
- MAN · alpha-D-mannopyranose · sugar · 8 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, O, E, P, H, S, K, T, L
- GAL · beta-D-galactopyranose · sugar · 6 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains B, E, K
- BMA · beta-D-mannopyranose · sugar · 4 copies
- CA · Calcium ion · metal · 8 copies · chains B, C, E, F, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.79 | 0.81 | 64 | empty |
| 2 | 131 | 0.77 | 0.96 | 30 | empty |
| 3 | 293 | 0.77 | 0.88 | 51 | empty |
| 4 | 103 | 0.75 | 0.96 | 27 | empty |
| 5 | 701 | 0.74 | 0.79 | 73 | empty |
Interfaces
36 interfaces between chains.
- J–K · 3581 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 3555 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 3538 Ų buried · 34 hydrogen bonds · protein-protein
- H–I · 3528 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3498 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3GHG · Crystal Structure of Human Fibrinogen · the same entry in another collection · chain K against K, 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
- Every structure of UniProt P02679
- Elsewhere: RCSB PDB 3GHG · PDBe 3GHG · UniProt P02671 · UniProt P02675 · UniProt P02679
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