Research workbench
Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4 ångströms resolution
Analyse Crystal structure of the central region of bovine fibrinogen (E5 fragment) at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JY3
- Type
- protein
- Length
- 283 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen gamma-B chain
- UniProt
- P02676, P12799
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N, Q | Fibrinogen alpha chain | protein | 44 | 68% helix, 9% strand | — |
| O, R | Fibrinogen beta chain | protein | 51 | 53% helix, 12% strand | P02676 |
| P | Fibrinogen gamma-B chain | protein | 46 | 50% helix, 17% strand | P12799 |
| S | Fibrinogen gamma-B chain | protein | 47 | 62% helix, 6% strand | P12799 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.71 | 0.86 | 39 | empty |
| 2 | 103 | 0.40 | 0.76 | 17 | empty |
| 3 | 66 | 0.28 | 0.73 | 14 | empty |
Interfaces
14 interfaces between chains.
- Q–R · 902 Ų buried · 9 hydrogen bonds · protein-protein
- N–O · 880 Ų buried · 10 hydrogen bonds · protein-protein
- Q–S · 776 Ų buried · 9 hydrogen bonds · protein-protein
- P–S · 764 Ų buried · 5 hydrogen bonds · protein-protein
- O–P · 758 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1JY3 · Crystal Structure of the Central Region of Bovine Fibrinogen (E5 Fragment) at 1.4… · the same entry in another collection · chain S against S, TM-score 1.00
- P02676 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (P02676) · a predicted model of the same protein · chain O against A, TM-score 0.82
- P12799 · AlphaFold monomer V2.0 prediction for fibrinogen gamma-B chain (P12799) · a predicted model of the same protein · chain S against A, TM-score 0.75
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 P02676
- Every structure of UniProt P12799
- Elsewhere: RCSB PDB 1JY3 · PDBe 1JY3 · UniProt P02676 · UniProt P12799
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.