MolNFT v1 · #191512 · protein
Crystal structure of human alpha-thrombin inhibited with SEL2770.
8KME: “Crystal structure of human alpha-thrombin inhibited with SEL2770.”. X-ray diffraction, 3 ligands (ACE, NA, NH2), 2 pockets (best druggability 0.38). MolNFT v1 #191512 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8KME
- Type
- protein
- Length
- 291 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; N-acetylhirudin; SEL2770
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- ACE, NA, NH2
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Thrombin (EC 3.4.21.5) | protein | 26 | 31% helix, 0% strand | P00734 |
| 2 | Thrombin (EC 3.4.21.5) | protein | 250 | 14% helix, 34% strand | P00734 |
| 3 | N-acetylhirudin | protein | 10 | 30% helix, 0% strand | — |
| 4 | SEL2770 | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains 2, 4
- NA · Sodium ion · metal · 2 copies · chains 2
- NH2 · Amino group · ion · chains 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.38 | 0.77 | 19 | empty |
| 2 | 76 | 0.37 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- 1–2 · 1114 Ų buried · 21 hydrogen bonds · protein-protein
- 2–3 · 608 Ų buried · 6 hydrogen bonds · protein-protein
- 2–4 · 510 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified, 1 covalent (disulfide, nonstandard, covalent ligand, methylation, sulfation).
Compared structures
- 8KME · Crystal structure of human alpha-thrombin inhibited with SEL2770. · the same entry in another collection · chain 1 against 1, 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 8KME · PDBe 8KME · UniProt P00734
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