MolNFT v1 · #118237 · protein + DNA
Human thrombin sandwiched between two DNA aptamers: HD22 and HD1- DELTAT3
5EW1 · Thrombin light chain: “Human thrombin sandwiched between two DNA aptamers: HD22 and HD1- DELTAT3”. X-ray diffraction, 3 ligands (0G6, NAG, NA), 5 pockets (best druggability 0.61). MolNFT v1 #118237 on GenesisL1: 3D structure…
- PDB
- 5EW1
- Type
- protein + DNA
- Length
- 318 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-DELTAT3
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, NA
- Pockets
- 5 · best druggability 0.61
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 | 26 | 38% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| D | HD22 (27MER) | dna | 26 | — | — |
| E | HD1-DELTAT3 | 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 · 2 copies · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.61 | 0.80 | 27 | empty |
| 2 | 122 | 0.52 | 0.82 | 19 | empty |
| 3 | 173 | 0.49 | 0.77 | 30 | 0G6 |
| 4 | 96 | 0.31 | 0.72 | 19 | empty |
| 5 | 54 | 0.26 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–D · 1139 Ų buried · 34 hydrogen bonds · protein-nucleic
- L–H · 1107 Ų buried · 27 hydrogen bonds · protein-protein
- H–E · 534 Ų buried · 14 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 5EW1 · PDBe 5EW1 · UniProt P00734
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