Research workbench
Crystal structure of the colicin E9, mutant HIS103ALA, in complex with MG+2 and dsdna (resolution 2.9A)
Analyse Crystal structure of the colicin E9, mutant HIS103ALA, in complex with MG+2 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V14
- Type
- protein + DNA
- Length
- 582 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin E9; 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
- EC
- 3.1.21.1
- UniProt
- P09883
- Ligands
- MG
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Colicin E9 (EC 3.1.21.1) | protein | 132 | 33% helix, 16% strand | P09883 |
| B | Colicin E9 (EC 3.1.21.1) | protein | 132 | 37% helix, 15% strand | P09883 |
| D | Colicin E9 (EC 3.1.21.1) | protein | 130 | 42% helix, 16% strand | P09883 |
| E, G, I, K | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' | dna | 6 | — | — |
| F, H, J, L | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' | dna | 8 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, E, C, I, G, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.72 | 0.85 | 39 | empty |
| 2 | 492 | 0.72 | 0.81 | 33 | empty |
| 3 | 719 | 0.66 | 0.75 | 75 | empty |
| 4 | 167 | 0.61 | 0.84 | 27 | empty |
| 5 | 70 | 0.55 | 0.88 | 13 | empty |
Interfaces
25 interfaces between chains.
- D–K · 532 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–G · 516 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–I · 505 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 504 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–H · 430 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 1V14 · Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA… · the same entry in another collection · chain L against L, 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 P09883
- Elsewhere: RCSB PDB 1V14 · PDBe 1V14 · UniProt P09883
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