MolNFT v1 · #24631 · protein + DNA
Crystal structure of the colicin E9, mutant HIS103ALA, in complex with ZN+2 and dsdna (resolution 2.4A)
1V15: “Crystal structure of the colicin E9, mutant HIS103ALA, in complex with ZN+2 and dsdna (resolution 2.4A)”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.77). MolNFT v1 #24631 on GenesisL1: 3D structure, binding…
- PDB
- 1V15
- Type
- protein + DNA
- Length
- 560 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
- ZN
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colicin E9 (EC 3.1.21.1) | protein | 106 | 27% helix, 14% strand | P09883 |
| B | Colicin E9 (EC 3.1.21.1) | protein | 134 | 39% helix, 16% strand | P09883 |
| C | Colicin E9 (EC 3.1.21.1) | protein | 129 | 35% helix, 16% strand | P09883 |
| D | Colicin E9 (EC 3.1.21.1) | protein | 133 | 38% helix, 16% strand | P09883 |
| E, I | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' | dna | 7 | — | — |
| F, H, J, L | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' | dna | 8 | — | — |
| G, K | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' | dna | 6 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, E, B, G, C, I, D, K, L, J, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.77 | 0.80 | 76 | ZN |
| 2 | 857 | 0.76 | 0.80 | 55 | ZN |
| 3 | 109 | 0.55 | 0.84 | 14 | empty |
| 4 | 113 | 0.54 | 0.83 | 27 | empty |
| 5 | 162 | 0.53 | 0.80 | 24 | empty |
Interfaces
32 interfaces between chains.
- D–K · 547 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–G · 522 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–E · 513 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–I · 508 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–F · 445 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1V15 · Crystal structure of the colicin E9, mutant HIS103ALA, in complex with ZN+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 1V15 · PDBe 1V15 · UniProt P09883
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