MolNFT v1 · #148168 · protein
Crystal structure of the pyoverdine maturation protein pvdp in complex with the mock substrates L-tyrosine and zinc.
6EYV: “Crystal structure of the pyoverdine maturation protein pvdp in complex with the mock substrates L-tyrosine…”. X-ray diffraction, 2 ligands (TYR, ZN), 12 pockets (best druggability 0.88). MolNFT v1 #148168 on GenesisL1: 3D structure…
- PDB
- 6EYV
- Type
- protein
- Length
- 916 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pvdp
- UniProt
- A0A0H2ZBG1
- Ligands
- TYR, ZN
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pvdp | protein | 457 | 38% helix, 16% strand | A0A0H2ZBG1 |
| A | Pvdp | protein | 459 | 38% helix, 16% strand | A0A0H2ZBG1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.88 | 0.91 | 91 | empty |
| 2 | 133 | 0.69 | 0.90 | 29 | empty |
| 3 | 378 | 0.64 | 0.78 | 37 | ZN, TYR |
| 4 | 319 | 0.60 | 0.78 | 39 | ZN, TYR |
| 5 | 189 | 0.52 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- B–A · 2970 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 6EYV · Crystal structure of the pyoverdine maturation protein PvdP in complex with the mock… · the same entry in another collection · chain B against B, 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 A0A0H2ZBG1
- Elsewhere: RCSB PDB 6EYV · PDBe 6EYV · UniProt A0A0H2ZBG1
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