MolNFT v1 · #61151 · protein + RNA
Crystal structure of an RNA aptamer bound to human thrombin
3DD2 · Thrombin light chain: “Crystal structure of an RNA aptamer bound to human thrombin”. X-ray diffraction, 2 ligands (0G6, MG), 5 pockets (best druggability 0.71). MolNFT v1 #61151 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3DD2
- Type
- protein + RNA
- Length
- 313 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; RNA (26-mer)
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain | protein | 30 | 40% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 258 | 17% helix, 34% strand | P00734 |
| B | RNA (26-mer) | rna | 25 | — | — |
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
- MG · Magnesium ion · metal · 2 copies · chains H, B
- ACY · Acetic acid · additive · 6 copies · chains H, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains L, H, B
- P6G · Hexaethylene glycol · additive · chains H
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 | 132 | 0.71 | 0.91 | 22 | empty |
| 2 | 189 | 0.51 | 0.77 | 39 | 0G6 |
| 3 | 237 | 0.49 | 0.75 | 24 | ACY |
| 4 | 138 | 0.43 | 0.75 | 20 | empty |
| 5 | 67 | 0.43 | 0.82 | 17 | MG |
Interfaces
2 interfaces between chains.
- L–H · 1206 Ų buried · 29 hydrogen bonds · protein-protein
- H–B · 957 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 10 modified, 4 disulfide, 2 covalent (nucleotide modification, disulfide, covalent ligand).
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 3DD2 · PDBe 3DD2 · UniProt P00734
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