MolNFT v1 · #103976 · protein
Crystal structure of a modulator protein mzra (KPN_03524) from klebsiella pneumoniae subsp. pneumoniae mgh 78578 at 2.45 a resolution
4PWU: “Crystal structure of a modulator protein mzra (KPN_03524) from klebsiella pneumoniae subsp. pneumoniae mgh…”. X-ray diffraction, 3 pockets (best druggability 0.51). MolNFT v1 #103976 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4PWU
- Type
- protein
- Length
- 307 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Modulator protein mzra
- UniProt
- A6TED5
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Modulator protein mzra | protein | 76 | 32% helix, 32% strand | A6TED5 |
| B | Modulator protein mzra | protein | 77 | 31% helix, 32% strand | A6TED5 |
| C | Modulator protein mzra | protein | 78 | 31% helix, 32% strand | A6TED5 |
| D | Modulator protein mzra | protein | 76 | 32% helix, 33% strand | A6TED5 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.51 | 0.75 | 38 | empty |
| 2 | 101 | 0.35 | 0.73 | 16 | GOL |
| 3 | 52 | 0.30 | 0.76 | 17 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 530 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 495 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 219 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4PWU · Crystal structure of a modulator protein MzrA (KPN_03524) from Klebsiella pneumoniae… · the same entry in another collection · chain D against D, TM-score 1.00
- A6TED5 · AlphaFold monomer V2.0 prediction for modulator protein mzra (A6TED5) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 A6TED5
- Elsewhere: RCSB PDB 4PWU · PDBe 4PWU · UniProt A6TED5
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