MolNFT v1 · #125357 · protein
Disulfated madanin-thrombin complex
5L6N · Prothrombin: “Disulfated madanin-thrombin complex”. X-ray diffraction, 2 ligands (NAG, NA), 3 pockets (best druggability 0.44). MolNFT v1 #125357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L6N
- Type
- protein
- Length
- 307 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Thrombin inhibitor madanin 1
- EC
- 3.4.21.5
- UniProt
- P00734, Q86FP9
- Ligands
- NAG, NA
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 29 | 45% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 254 | 15% helix, 34% strand | P00734 |
| I | Thrombin inhibitor madanin 1 | protein | 24 | 0% helix, 4% strand | Q86FP9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.44 | 0.77 | 27 | empty |
| 2 | 84 | 0.38 | 0.77 | 21 | empty |
| 3 | 56 | 0.27 | 0.73 | 12 | empty |
Interfaces
2 interfaces between chains.
- H–I · 1432 Ų buried · 22 hydrogen bonds · protein-protein
- L–H · 1132 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified, 1 glycan (disulfide, sulfation, N-glycosylation).
Compared structures
- 5L6N · Disulfated madanin-thrombin complex · the same entry in another collection · chain L against L, TM-score 1.00
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 Q86FP9
- Elsewhere: RCSB PDB 5L6N · PDBe 5L6N · UniProt P00734 · UniProt Q86FP9
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