MolNFT v1 · #72234 · protein
Crystal structure of prolidase EAH89906 complexed with N- methylphosphonate-L-proline
3N2C: “Crystal structure of prolidase EAH89906 complexed with N- methylphosphonate-L-proline”. X-ray diffraction, 2 ligands (LWY, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #72234 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3N2C
- Type
- protein
- Length
- 6,528 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolidase
- Ligands
- LWY, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Prolidase | protein | 408 | 35% helix, 24% strand | — |
Ligands and binding sites
- LWY · 1-[(R)-hydroxy(methyl)phosphoryl]-L-proline · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- ZN · Zinc ion · metal · 32 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.84 | 0.85 | 136 | empty |
| 2 | 942 | 0.83 | 0.84 | 107 | empty |
| 3 | 278 | 0.82 | 0.93 | 55 | empty |
| 4 | 639 | 0.81 | 0.86 | 75 | empty |
| 5 | 598 | 0.81 | 0.86 | 75 | empty |
Interfaces
37 interfaces between chains.
- E–F · 818 Ų buried · 1 hydrogen bond · protein-protein
- D–G · 817 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 814 Ų buried · 0 hydrogen bonds · protein-protein
- I–J · 800 Ų buried · 0 hydrogen bonds · protein-protein
- C–H · 792 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (carboxylation).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3N2C · PDBe 3N2C
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