Research workbench
Human plasma coagulation fxi with peptide LP2
Analyse Human plasma coagulation fxi with peptide LP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EOD
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor XI; LP2
- EC
- 3.4.21.27
- UniProt
- P03951
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor XI (EC 3.4.21.27) | protein | 586 | 16% helix, 37% strand | P03951 |
| B | LP2 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.81 | 0.86 | 62 | empty |
| 2 | 472 | 0.71 | 0.81 | 42 | empty |
| 3 | 368 | 0.64 | 0.79 | 49 | empty |
| 4 | 176 | 0.57 | 0.81 | 30 | empty |
| 5 | 99 | 0.39 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 468 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 P03951
- Elsewhere: RCSB PDB 5EOD · PDBe 5EOD · UniProt P03951
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