MolNFT v1 · #127085 · protein
Thrombin mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4- CARBAMIMIDOYLBENZYL)PYRROLIDINE-2-carboxamide
5MM6 · Thrombin light chain: “Thrombin mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4…”. X-ray diffraction, 3 ligands (32U, NA, PO4), 2 pockets (best druggability 0.52). MolNFT v1 #127085 on GenesisL1: 3D structure, binding sites…
- PDB
- 5MM6
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- 32U, NA, PO4
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 27% helix, 0% strand | P09945 |
Ligands and binding sites
- 32U · D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide · ligand · chains H
- NA · Sodium ion · metal · 2 copies · chains H
- PO4 · Phosphate ion · ion · chains H
- GOL · Glycerol · additive · 5 copies · chains H
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.52 | 0.77 | 37 | GOL, 32U |
| 2 | 54 | 0.27 | 0.74 | 11 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1109 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 632 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 5MM6 · Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrr… · 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 P09945
- Elsewhere: RCSB PDB 5MM6 · PDBe 5MM6 · UniProt P00734 · UniProt P09945
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