MolNFT v1 · #185399 · protein
Structure of hexameric S-layer protein from haloferax volcanii archaea
7PTR · Cell surface glycoprotein: “Structure of hexameric S-layer protein from haloferax volcanii archaea”. Electron microscopy, 2 ligands (BGC, CA), 20 pockets (best druggability 0.72). MolNFT v1 #185399 on GenesisL1: 3D structure…
- PDB
- 7PTR
- Type
- protein
- Length
- 4,350 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell surface glycoprotein
- UniProt
- P25062
- Ligands
- BGC, CA
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 1 distinct chain · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Cell surface glycoprotein | protein | 725 | 10% helix, 40% strand | P25062 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.72 | 0.76 | 108 | empty |
| 2 | 938 | 0.71 | 0.76 | 91 | empty |
| 3 | 952 | 0.70 | 0.75 | 92 | empty |
| 4 | 959 | 0.70 | 0.75 | 105 | empty |
| 5 | 830 | 0.68 | 0.75 | 88 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1435 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1434 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1431 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1427 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 1427 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan (N-glycosylation).
Compared structures
- 7PTR · Structure of hexameric S-layer protein from Haloferax volcanii archaea · the same entry in another collection · chain F against F, TM-score 1.00
- P25062 · AlphaFold monomer V2.0 prediction for cell surface glycoprotein (P25062) · a predicted model of the same protein · chain F against A, TM-score 0.74
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 P25062
- Elsewhere: RCSB PDB 7PTR · PDBe 7PTR · UniProt P25062
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