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Structure of the K. pneumonia slma-DNA complex bound to the C-terminal of the cell division protein ftsz
Analyse Structure of the K. pneumonia slma-DNA complex bound to the C-terminal of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K58
- Type
- protein + DNA
- Length
- 814 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoid occlusion factor slma; DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')…
- UniProt
- A7ZTJ2
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A | Nucleoid occlusion factor slma | protein | 190 | 71% helix, 0% strand | A7ZTJ2 |
| F, B | Nucleoid occlusion factor slma | protein | 189 | 74% helix, 0% strand | A7ZTJ2 |
| R, T | DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3') | dna | 12 | — | — |
| L, K, N, M | Octapeptide | protein | 8 | 0% helix, 0% strand | — |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.68 | 0.94 | 21 | empty |
| 2 | 402 | 0.58 | 0.75 | 33 | empty |
| 3 | 337 | 0.54 | 0.75 | 33 | empty |
| 4 | 60 | 0.53 | 0.88 | 19 | empty |
| 5 | 60 | 0.51 | 0.87 | 18 | empty |
Interfaces
16 interfaces between chains.
- E–F · 1849 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1719 Ų buried · 26 hydrogen bonds · protein-protein
- F–M · 659 Ų buried · 5 hydrogen bonds · protein-protein
- B–K · 640 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 569 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5K58 · Structure of the K. pneumonia SlmA-DNA complex bound to the C-terminal of the cell… · the same entry in another collection · chain F against F, TM-score 1.00
- A7ZTJ2 · AlphaFold monomer V2.0 prediction for nucleoid occlusion factor slma (A7ZTJ2) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 A7ZTJ2
- Elsewhere: RCSB PDB 5K58 · PDBe 5K58 · UniProt A7ZTJ2
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