MolNFT v1 · #148165 · protein
Crystal structure of the periplasmic pyoverdine maturation protein pvdp
6EYS: “Crystal structure of the periplasmic pyoverdine maturation protein pvdp”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #148165 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EYS
- Type
- protein
- Length
- 1,889 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pvdp
- UniProt
- A0A0H2ZBG1
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pvdp | protein | 478 | 35% helix, 15% strand | A0A0H2ZBG1 |
| A | Pvdp | protein | 469 | 36% helix, 15% strand | A0A0H2ZBG1 |
| C | Pvdp | protein | 470 | 36% helix, 15% strand | A0A0H2ZBG1 |
| D | Pvdp | protein | 472 | 35% helix, 15% strand | A0A0H2ZBG1 |
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.88 | 0.90 | 133 | empty |
| 2 | 960 | 0.88 | 0.90 | 119 | empty |
| 3 | 1127 | 0.73 | 0.77 | 99 | empty |
| 4 | 58 | 0.50 | 0.86 | 15 | empty |
| 5 | 109 | 0.49 | 0.80 | 32 | empty |
Interfaces
4 interfaces between chains.
- B–A · 3380 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3345 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 408 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EYS · Crystal structure of the periplasmic pyoverdine maturation protein PvdP · 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 6EYS · PDBe 6EYS · UniProt A0A0H2ZBG1
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