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Substrate bound neisseria ap endonuclease in absence of metal ions (crystal form 2)
Analyse Substrate bound neisseria ap endonuclease in absence of metal ions (crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B5G
- Type
- protein + DNA
- Length
- 843 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease; 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'…
- EC
- 3.1.11.2
- UniProt
- C9X331
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 259 | 25% helix, 27% strand | C9X331 |
| U, W, Y | 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3' | dna | 11 | — | — |
| V, X, Z | 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3' | dna | 11 | — | — |
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.75 | 0.81 | 74 | empty |
| 2 | 202 | 0.63 | 0.84 | 42 | empty |
| 3 | 528 | 0.60 | 0.74 | 38 | empty |
| 4 | 143 | 0.56 | 0.83 | 30 | empty |
| 5 | 78 | 0.46 | 0.81 | 14 | empty |
Interfaces
18 interfaces between chains.
- B–W · 766 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–U · 757 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–Y · 749 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–X · 543 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–V · 513 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 4B5G · Substrate bound Neisseria AP endonuclease in absence of metal ions (crystal 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 C9X331
- Elsewhere: RCSB PDB 4B5G · PDBe 4B5G · UniProt C9X331
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