Research workbench
Crystal structure of thrombin in complex with fibrinogen gamma' peptide
Analyse Crystal structure of thrombin in complex with fibrinogen gamma' peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HWL
- Type
- protein
- Length
- 576 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Fibrinogen gamma' peptide
- EC
- 3.4.21.5
- UniProt
- P00734, P02679
- Ligands
- NAG, NA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 27 | 30% helix, 0% strand | P00734 |
| B, D | Prothrombin (EC 3.4.21.5) | protein | 251 | 13% helix, 34% strand | P00734 |
| C | Prothrombin (EC 3.4.21.5) | protein | 33 | 24% helix, 0% strand | P00734 |
| P | Fibrinogen gamma' peptide | protein | 14 | 0% helix, 0% strand | P02679 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains D
- NA · Sodium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.82 | 0.83 | 93 | empty |
| 2 | 51 | 0.53 | 0.88 | 16 | empty |
| 3 | 62 | 0.39 | 0.80 | 14 | empty |
| 4 | 57 | 0.30 | 0.75 | 14 | empty |
| 5 | 60 | 0.29 | 0.73 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1342 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1057 Ų buried · 24 hydrogen bonds · protein-protein
- D–P · 821 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 806 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified, 1 glycan (disulfide, phosphorylation, N-glycosylation).
Compared structures
- 2HWL · Crystal structure of thrombin in complex with fibrinogen gamma' peptide · the same entry in another collection · chain B against B, TM-score 1.00
- P02679 · AlphaFold monomer V2.0 prediction for fibrinogen gamma chain (P02679) · a predicted model of the same protein · chain P against A, TM-score 0.26
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 P00734
- Every structure of UniProt P02679
- Elsewhere: RCSB PDB 2HWL · PDBe 2HWL · UniProt P00734 · UniProt P02679
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