MolNFT v1 · #65505 · protein
The ectoine binding protein of the teaabc trap transporter teaa in the apo-state
3GYY · Periplasmic substrate binding protein: “The ectoine binding protein of the teaabc trap transporter teaa in the apo-state”. X-ray diffraction, 1 ligand (ZN), 14 pockets (best druggability 0.69). MolNFT v1 #65505 on GenesisL1: 3D…
- PDB
- 3GYY
- Type
- protein
- Length
- 1,231 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic substrate binding protein
- UniProt
- Q8VPB3
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic substrate binding protein | protein | 304 | 54% helix, 18% strand | Q8VPB3 |
| B | Periplasmic substrate binding protein | protein | 307 | 53% helix, 17% strand | Q8VPB3 |
| C | Periplasmic substrate binding protein | protein | 309 | 53% helix, 18% strand | Q8VPB3 |
| D | Periplasmic substrate binding protein | protein | 311 | 52% helix, 18% strand | Q8VPB3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 36 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.69 | 0.77 | 69 | ZN |
| 2 | 634 | 0.69 | 0.77 | 50 | ZN |
| 3 | 369 | 0.63 | 0.78 | 47 | empty |
| 4 | 365 | 0.62 | 0.78 | 40 | ZN |
| 5 | 251 | 0.57 | 0.78 | 30 | empty |
Interfaces
4 interfaces between chains.
- B–C · 476 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 316 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 284 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 49 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3GYY · The ectoine binding protein of the TeaABC TRAP transporter TeaA in the Apo-State · the same entry in another collection · chain C against C, 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 Q8VPB3
- Elsewhere: RCSB PDB 3GYY · PDBe 3GYY · UniProt Q8VPB3
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