MolNFT v1 · #62757 · protein
Structure of the pgrp-hd from alvinella pompejana
3EP1 · Pgrp-hd - peptidoglycan recognition protein homologue: “Structure of the pgrp-hd from alvinella pompejana”. X-ray diffraction, 3 pockets (best druggability 0.52). MolNFT v1 #62757 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3EP1
- Type
- protein
- Length
- 331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pgrp-hd - peptidoglycan recognition protein homologue
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pgrp-hd - peptidoglycan recognition protein homologue | protein | 167 | 30% helix, 19% strand | — |
| B | Pgrp-hd - peptidoglycan recognition protein homologue | protein | 164 | 26% helix, 19% strand | — |
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 | 194 | 0.52 | 0.77 | 32 | empty |
| 2 | 101 | 0.36 | 0.74 | 24 | empty |
| 3 | 63 | 0.33 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3EP1 · Structure of the PGRP-Hd from Alvinella pompejana · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3EP1 · PDBe 3EP1
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