Research workbench
X-ray structure of the complex between human thrombin and the tba deletion mutant lacking thymine 12 nucleobase
Analyse X-ray structure of the complex between human thrombin and the tba deletion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LZ1
- Type
- protein + DNA
- Length
- 292 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Thrombin binding aptamer
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, K, NA
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 43% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 14% helix, 36% strand | P00734 |
| D | Thrombin binding aptamer | 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
- K · Potassium ion · metal · chains D
- NA · Sodium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.55 | 0.78 | 35 | 0G6 |
| 2 | 57 | 0.31 | 0.76 | 20 | empty |
| 3 | 53 | 0.28 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1125 Ų buried · 26 hydrogen bonds · protein-protein
- H–D · 542 Ų buried · 23 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, nucleotide modification).
Compared structures
- 4LZ1 · X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking… · the same entry in another collection · chain L against L, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.92
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 4LZ1 · PDBe 4LZ1 · UniProt P00734
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