MolNFT v1 · #89740 · protein
Crystal structures of protease nexin-1 in complex with S195A thrombin
4DY7 · Thrombin light chain: “Crystal structures of protease nexin-1 in complex with S195A thrombin”. X-ray diffraction, 2 ligands (CA, NA), 11 pockets (best druggability 0.78). MolNFT v1 #89740 on GenesisL1: 3D structure, binding sites…
- PDB
- 4DY7
- Type
- protein
- Length
- 1,343 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Glia-derived nexin
- EC
- 3.4.21.5
- UniProt
- P00734, P07093
- Ligands
- CA, NA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 45 | 40% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 253 | 13% helix, 34% strand | P00734 |
| C | Glia-derived nexin | protein | 377 | 31% helix, 32% strand | P07093 |
| D | Thrombin light chain (EC 3.4.21.5) | protein | 39 | 13% helix, 0% strand | P00734 |
| E | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 12% helix, 33% strand | P00734 |
| F | Glia-derived nexin | protein | 378 | 34% helix, 32% strand | P07093 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, F
- NA · Sodium ion · metal · chains B
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.78 | 0.83 | 81 | empty |
| 2 | 858 | 0.75 | 0.79 | 90 | empty |
| 3 | 322 | 0.62 | 0.79 | 35 | empty |
| 4 | 323 | 0.60 | 0.78 | 41 | empty |
| 5 | 53 | 0.57 | 0.90 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1716 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1067 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 867 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 805 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 63 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
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
- Every structure of UniProt P07093
- Elsewhere: RCSB PDB 4DY7 · PDBe 4DY7 · UniProt P00734 · UniProt P07093
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