MolNFT v1 · #27538 · protein
Crystal structure of thrombin bound to heparin
1XMN · Thrombin light chain: “Crystal structure of thrombin bound to heparin”. X-ray diffraction, 8 ligands (0G6, SGN, NAG), 14 pockets (best druggability 0.61). MolNFT v1 #27538 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1XMN
- Type
- protein
- Length
- 1,140 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, SGN, NAG, IDS, NDG, MAN, BMA, NA
- Pockets
- 14 · best druggability 0.61
Structure
x-ray diffraction · 8 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 31 | 32% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 256 | 15% helix, 34% strand | P00734 |
| C | Thrombin light chain (EC 3.4.21.5) | protein | 32 | 31% helix, 0% strand | P00734 |
| D | Thrombin heavy chain (EC 3.4.21.5) | protein | 254 | 15% helix, 34% strand | P00734 |
| E | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| F | Thrombin heavy chain (EC 3.4.21.5) | protein | 254 | 14% helix, 34% strand | P00734 |
| G | Thrombin light chain (EC 3.4.21.5) | protein | 31 | 32% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 253 | 15% helix, 34% strand | P00734 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 4 copies · chains B, D, F, H
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 6 copies · chains B, H, D, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D, F, H
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 5 copies · chains H, B, D, F
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains F
- BMA · beta-D-mannopyranose · sugar
- NA · Sodium ion · metal · 4 copies · chains B, D, F, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.61 | 0.88 | 17 | empty |
| 2 | 325 | 0.60 | 0.78 | 42 | 0G6 |
| 3 | 274 | 0.58 | 0.78 | 37 | 0G6 |
| 4 | 261 | 0.58 | 0.78 | 36 | 0G6 |
| 5 | 294 | 0.57 | 0.77 | 40 | 0G6 |
Interfaces
7 interfaces between chains.
- A–B · 1235 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1205 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1195 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1155 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 525 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 covalent, 4 glycan (disulfide, covalent ligand, N-glycosylation).
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 1XMN · PDBe 1XMN · UniProt P00734
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