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Crystal structure of proline utilization a (puta) from bdellovibrio bacteriovorus inactivated by N-propargylglycine
Analyse Crystal structure of proline utilization a (puta) from bdellovibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UR2
- Type
- protein
- Length
- 3,832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein puta
- UniProt
- Q6MNK1
- Ligands
- P5F
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein puta | protein | 956 | 48% helix, 17% strand | Q6MNK1 |
| B | Bifunctional protein puta | protein | 959 | 48% helix, 17% strand | Q6MNK1 |
| C | Bifunctional protein puta | protein | 958 | 48% helix, 17% strand | Q6MNK1 |
| D | Bifunctional protein puta | protein | 959 | 48% helix, 17% strand | Q6MNK1 |
Ligands and binding sites
- P5F · N-propargylglycine-modified flavin adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.87 | 0.89 | 86 | P5F |
| 2 | 899 | 0.87 | 0.89 | 80 | P5F |
| 3 | 418 | 0.87 | 0.95 | 54 | empty |
| 4 | 775 | 0.87 | 0.90 | 74 | P5F |
| 5 | 806 | 0.86 | 0.89 | 76 | P5F |
Interfaces
4 interfaces between chains.
- A–B · 4115 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 4075 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 191 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5UR2 · Crystal structure of proline utilization A (PutA) from Bdellovibrio bacteriovorus… · the same entry in another collection · chain A against A, 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 Q6MNK1
- Elsewhere: RCSB PDB 5UR2 · PDBe 5UR2 · UniProt Q6MNK1
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