Research workbench
Complex between DNA and the DNA photolyase from anacystis nidulans
Analyse Complex between DNA and the DNA photolyase from anacystis nidulans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TEZ
- Type
- protein + DNA
- Length
- 1,954 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'; 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'…
- EC
- 4.1.99.3
- UniProt
- P05327
- Ligands
- FAD, HDF, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, K | 5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3' | dna | 11 | — | — |
| J, L | 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3' | dna | 9 | — | — |
| M, O | 5'-D(*TP*CP*GP*C)-3' | dna | 4 | — | — |
| N, P | 5'-D(P*GP*CP*CP*GP*A)-3' | dna | 5 | — | — |
| A, B, C, D | Deoxyribodipyrimidine photolyase (EC 4.1.99.3) | protein | 474 | 54% helix, 6% strand | P05327 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains I, A, K, B, C, D
- HDF · 8-hydroxy-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)-5-deazaisoalloxazine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains J, A, L, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.86 | 0.94 | 41 | FAD |
| 2 | 447 | 0.86 | 0.93 | 41 | FAD |
| 3 | 786 | 0.83 | 0.86 | 59 | FAD |
| 4 | 730 | 0.82 | 0.86 | 56 | FAD |
| 5 | 456 | 0.79 | 0.87 | 48 | empty |
Interfaces
13 interfaces between chains.
- I–A · 602 Ų buried · 12 hydrogen bonds · protein-nucleic
- K–B · 598 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 558 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 556 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 554 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1TEZ · Complex between DNA and the DNA photolyase from anacystis nidulans · the same entry in another collection · chain D against D, 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 P05327
- Elsewhere: RCSB PDB 1TEZ · PDBe 1TEZ · UniProt P05327
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