Research workbench
Madanins (merops I53) are cleaved by thrombin and factor xa
Analyse Madanins (merops I53) are cleaved by thrombin and factor xa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BOH
- Type
- protein
- Length
- 571 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin heavy chain; Thrombin light chain; Thrombin inhibitor madanin 1
- EC
- 3.4.21.5
- UniProt
- P00734, Q86FP9
- Ligands
- NAG, NA, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 15% helix, 35% strand | P00734 |
| B | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 32% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 258 | 15% helix, 34% strand | P00734 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 32 | 28% helix, 0% strand | P00734 |
| M | Thrombin inhibitor madanin 1 | protein | 4 | 0% helix, 0% strand | Q86FP9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, H
- NA · Sodium ion · metal · 2 copies · chains A, H
- SO4 · Sulfate ion · ion · 5 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.76 | 0.78 | 73 | SO4 |
| 2 | 244 | 0.54 | 0.77 | 44 | empty |
| 3 | 185 | 0.53 | 0.79 | 23 | empty |
| 4 | 64 | 0.29 | 0.73 | 17 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1245 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1095 Ų buried · 25 hydrogen bonds · protein-protein
- H–M · 502 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 264 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 124 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4BOH · Madanins (MEROPS I53) are cleaved by thrombin and factor Xa · the same entry in another collection · chain A against A, 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 4BOH · PDBe 4BOH · UniProt P00734 · UniProt Q86FP9
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