MolNFT v1 · #27887 · protein
Crystal structure of the fxia catalytic domain in complex with ECOTINM84R
1XX9 · Coagulation factor XI: “Crystal structure of the fxia catalytic domain in complex with ECOTINM84R”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.76). MolNFT v1 #27887 on GenesisL1: 3D structure, binding sites…
- PDB
- 1XX9
- Type
- protein
- Length
- 749 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor XI; Ecotin
- EC
- 3.4.21.27
- UniProt
- P03951, P23827
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor XI (EC 3.4.21.27) | protein | 237 | 12% helix, 36% strand | P03951 |
| B | Coagulation factor XI (EC 3.4.21.27) | protein | 233 | 13% helix, 35% strand | P03951 |
| C | Ecotin | protein | 140 | 7% helix, 54% strand | P23827 |
| D | Ecotin | protein | 139 | 7% helix, 54% strand | P23827 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.76 | 0.80 | 77 | empty |
| 2 | 1019 | 0.76 | 0.79 | 85 | empty |
| 3 | 234 | 0.54 | 0.77 | 43 | empty |
| 4 | 120 | 0.48 | 0.79 | 21 | empty |
| 5 | 136 | 0.45 | 0.77 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1713 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1212 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1103 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 671 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 629 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1XX9 · Crystal Structure of the FXIa Catalytic Domain in Complex with EcotinM84R · the same entry in another collection · chain D against D, TM-score 1.00
- P03951 · AlphaFold monomer V2.0 prediction for coagulation factor XI (P03951) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P23827 · AlphaFold monomer V2.0 prediction for ecotin (P23827) · a predicted model of the same protein · chain D against A, TM-score 0.96
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
- Every structure of UniProt P23827
- Elsewhere: RCSB PDB 1XX9 · PDBe 1XX9 · UniProt P03951 · UniProt P23827
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