Research workbench
Crystal structure of native chicken fibrinogen with two different bound ligands
Analyse Crystal structure of native chicken fibrinogen with two different bound ligands in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M1J
- Type
- protein
- Length
- 1,984 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen alpha subunit; Fibrinogen beta chain; Fibrinogen gamma chain; Gly-pro-arg-pro…
- UniProt
- P14448, Q02020, O93568
- Ligands
- NDG, NAG, CA
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen alpha subunit | protein | 192 | 60% helix, 2% strand | P14448 |
| B | Fibrinogen beta chain | protein | 402 | 39% helix, 21% strand | Q02020 |
| C | Fibrinogen gamma chain | protein | 390 | 35% helix, 20% strand | O93568 |
| D | Fibrinogen alpha subunit | protein | 194 | 52% helix, 2% strand | P14448 |
| E | Fibrinogen beta chain | protein | 401 | 32% helix, 21% strand | Q02020 |
| F | Fibrinogen gamma chain | protein | 389 | 28% helix, 21% strand | O93568 |
| G, H | Gly-pro-arg-pro peptide | protein | 4 | 0% helix, 0% strand | — |
| I, J | Gly-his-arg-pro peptide | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 5 copies · chains B, I, C, E, J, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies
- 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 | 734 | 0.83 | 0.87 | 63 | empty |
| 2 | 399 | 0.69 | 0.81 | 47 | empty |
| 3 | 294 | 0.58 | 0.77 | 37 | empty |
| 4 | 147 | 0.57 | 0.82 | 31 | empty |
| 5 | 148 | 0.57 | 0.82 | 24 | empty |
Interfaces
18 interfaces between chains.
- D–E · 4469 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 4403 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 3856 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 3791 Ų buried · 45 hydrogen bonds · protein-protein
- D–F · 2679 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
Compared structures
- 1M1J · Crystal structure of native chicken fibrinogen with two different bound ligands · the same entry in another collection · chain J against J, TM-score 1.00
- Q02020 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (Q02020) · a predicted model of the same protein · chain E 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 P14448
- Every structure of UniProt Q02020
- Every structure of UniProt O93568
- Elsewhere: RCSB PDB 1M1J · PDBe 1M1J · UniProt P14448 · UniProt Q02020 · UniProt O93568
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