Research workbench
Metal-depleted ECL18KI in complex with uncleaved, modified DNA
Analyse Metal-depleted ECL18KI in complex with uncleaved, modified DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GB7
- Type
- protein + DNA
- Length
- 1,209 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA strand 1; DNA strand 2; R.ECL18KI
- UniProt
- O87963
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 66% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | DNA strand 1 | dna | 9 | — | — |
| F, H | DNA strand 2 | dna | 9 | — | — |
| A | R.ECL18KI | protein | 293 | 65% helix, 9% strand | O87963 |
| B | R.ECL18KI | protein | 295 | 66% helix, 7% strand | O87963 |
| C | R.ECL18KI | protein | 293 | 68% helix, 9% strand | O87963 |
| D | R.ECL18KI | protein | 292 | 66% helix, 8% strand | O87963 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.77 | 0.82 | 68 | empty |
| 2 | 693 | 0.77 | 0.82 | 70 | empty |
| 3 | 581 | 0.76 | 0.83 | 65 | empty |
| 4 | 252 | 0.58 | 0.78 | 27 | empty |
| 5 | 197 | 0.57 | 0.80 | 24 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1879 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1874 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 948 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 937 Ų buried · 26 hydrogen bonds · protein-protein
- G–C · 834 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 2GB7 · Metal-depleted Ecl18kI in complex with uncleaved, modified DNA · the same entry in another collection · chain E against E, 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 O87963
- Elsewhere: RCSB PDB 2GB7 · PDBe 2GB7 · UniProt O87963
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