MolNFT v1 · #119812 · protein
Hirunorms are true hirudin mimetics. the crystal structure of human alpha-THROMBIN:HIRUNORM V complex
5GDS: “Hirunorms are true hirudin mimetics. the crystal structure of human alpha-THROMBIN:HIRUNORM V complex”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.42). MolNFT v1 #119812 on GenesisL1: 3D structure, binding…
- PDB
- 5GDS
- Type
- protein
- Length
- 304 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Hirunorm V
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (EC 3.4.21.5) | protein | 36 | 28% helix, 0% strand | P00734 |
| H | Alpha-thrombin (EC 3.4.21.5) | protein | 253 | 15% helix, 36% strand | P00734 |
| I | Hirunorm V | protein | 15 | 0% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.42 | 0.76 | 23 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1559 Ų buried · 31 hydrogen bonds · protein-protein
- H–I · 1072 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 4 disulfide, 1 d-amino, 1 glycan (nonstandard, disulfide, D-amino acid, N-glycosylation).
Compared structures
- 5GDS · Hirunorms are true hirudin mimetics. the crystal structure of human… · 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
- Elsewhere: RCSB PDB 5GDS · PDBe 5GDS · UniProt P00734
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