MolNFT v1 · #167218 · protein
Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH
6VE1: “Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.76). MolNFT v1 #167218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VE1
- Type
- protein
- Length
- 1,069 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-N-acetylglucosaminidase H
- EC
- 3.2.1.96
- UniProt
- P04067
- Ligands
- MG
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-N-acetylglucosaminidase H (EC 3.2.1.96) | protein | 267 | 34% helix, 25% strand | P04067 |
| B, D | Endo-beta-N-acetylglucosaminidase H (EC 3.2.1.96) | protein | 267 | 34% helix, 25% strand | P04067 |
| C | Endo-beta-N-acetylglucosaminidase H (EC 3.2.1.96) | protein | 268 | 35% helix, 25% strand | P04067 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.76 | 0.78 | 127 | MG |
| 2 | 1129 | 0.76 | 0.78 | 127 | empty |
| 3 | 64 | 0.37 | 0.78 | 16 | empty |
| 4 | 60 | 0.34 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–C · 647 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 642 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 355 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 354 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6VE1 · Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH · the same entry in another collection · chain D against D, TM-score 1.00
- P04067 · AlphaFold monomer V2.0 prediction for endo-beta-N- acetylglucosaminidase H (P04067) · a predicted model of the same protein · 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
- Every structure of UniProt P04067
- Elsewhere: RCSB PDB 6VE1 · PDBe 6VE1 · UniProt P04067
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