Research workbench
Crystal structure of deinococcus radiodurans uvrd in complex with DNA, form 2
Analyse Crystal structure of deinococcus radiodurans uvrd in complex with DNA, form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C30
- Type
- protein + DNA
- Length
- 2,635 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA helicase II; DNA strand FOR25; DNA strand REV25
- EC
- 3.6.4.12
- UniProt
- Q9RTI9
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA helicase II (EC 3.6.4.12) | protein | 631 | 52% helix, 13% strand | Q9RTI9 |
| D | DNA helicase II (EC 3.6.4.12) | protein | 642 | 52% helix, 13% strand | Q9RTI9 |
| F | DNA helicase II (EC 3.6.4.12) | protein | 632 | 52% helix, 13% strand | Q9RTI9 |
| I | DNA helicase II (EC 3.6.4.12) | protein | 638 | 50% helix, 13% strand | Q9RTI9 |
| K, X | DNA strand FOR25 | dna | 23 | — | — |
| L, Y | DNA strand REV25 | dna | 23 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, F
- MG · Magnesium ion · metal · 6 copies · chains A, D, F, I
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 | 1111 | 0.82 | 0.83 | 108 | MG |
| 2 | 969 | 0.82 | 0.83 | 81 | empty |
| 3 | 1112 | 0.82 | 0.83 | 95 | MG |
| 4 | 1107 | 0.77 | 0.80 | 94 | empty |
| 5 | 1030 | 0.76 | 0.78 | 89 | empty |
Interfaces
11 interfaces between chains.
- A–X · 1146 Ų buried · 23 hydrogen bonds · protein-nucleic
- I–L · 1140 Ų buried · 16 hydrogen bonds · protein-nucleic
- F–K · 1139 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–Y · 1123 Ų buried · 18 hydrogen bonds · protein-nucleic
- K–L · 813 Ų buried · 90 hydrogen bonds · nucleic-nucleic
Compared structures
- 4C30 · Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, form 2 · 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 Q9RTI9
- Elsewhere: RCSB PDB 4C30 · PDBe 4C30 · UniProt Q9RTI9
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