MolNFT v1 · #118238 · protein + DNA
Human thrombin sandwiched between two DNA aptamers: HD22 and HD1- DELTAT12
5EW2 · Thrombin light chain: “Human thrombin sandwiched between two DNA aptamers: HD22 and HD1- DELTAT12”. X-ray diffraction, 3 ligands (0G6, NAG, NA), 5 pockets (best druggability 0.51). MolNFT v1 #118238 on GenesisL1: 3D structure…
- PDB
- 5EW2
- Type
- protein + DNA
- Length
- 319 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; HD22 (27MER); HD1-DELTAT12
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, NA
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 4 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 |
| D | HD22 (27MER) | dna | 25 | — | — |
| E | HD1-DELTAT12 | dna | 15 | — | — |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · 3 copies · chains H, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.51 | 0.77 | 31 | 0G6 |
| 2 | 241 | 0.50 | 0.76 | 25 | empty |
| 3 | 113 | 0.46 | 0.79 | 19 | empty |
| 4 | 139 | 0.39 | 0.73 | 15 | empty |
| 5 | 72 | 0.32 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1158 Ų buried · 25 hydrogen bonds · protein-protein
- H–D · 1070 Ų buried · 23 hydrogen bonds · protein-nucleic
- H–E · 536 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 modified (disulfide, covalent ligand, nucleotide modification).
Compared structures
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 5EW2 · PDBe 5EW2 · UniProt P00734
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