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Structure of the methanosarcina mazei class II cpd-photolyase in complex with intact, phosphodiester linked, cpd-lesion
Analyse Structure of the methanosarcina mazei class II cpd-photolyase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZCW
- Type
- protein + DNA
- Length
- 934 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribodipyrimidine photolyase; 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'…
- UniProt
- A0A0F8I5V2
- Ligands
- FAD, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribodipyrimidine photolyase | protein | 459 | 53% helix, 7% strand | A0A0F8I5V2 |
| B | Deoxyribodipyrimidine photolyase | protein | 429 | 54% helix, 8% strand | A0A0F8I5V2 |
| C | 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3' | dna | 13 | — | — |
| D | 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3' | dna | 14 | — | — |
| E | 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3' | dna | 9 | — | — |
| F | 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3' | dna | 10 | — | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, C, B, E
- SO4 · Sulfate ion · ion · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.88 | 0.89 | 107 | empty |
| 2 | 440 | 0.86 | 0.94 | 42 | FAD |
| 3 | 429 | 0.86 | 0.94 | 42 | FAD |
| 4 | 354 | 0.59 | 0.77 | 21 | empty |
| 5 | 86 | 0.52 | 0.84 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1255 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 790 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–E · 725 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 580 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–D · 549 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ZCW · Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact… · the same entry in another collection · chain F against F, 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 A0A0F8I5V2
- Elsewhere: RCSB PDB 5ZCW · PDBe 5ZCW · UniProt A0A0F8I5V2
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