Research workbench
MVNEI1-G86D
Analyse MVNEI1-G86D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NRW
- Type
- protein + DNA
- Length
- 622 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase; 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'…
- EC
- 3.2.2.23, 4.2.99.18
- UniProt
- Q5UQ00
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 285 | 29% helix, 21% strand | Q5UQ00 |
| C, E | 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' | dna | 13 | — | — |
| D, F | 5'-D(*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3' | dna | 13 | — | — |
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.74 | 0.78 | 68 | empty |
| 2 | 520 | 0.64 | 0.76 | 47 | empty |
| 3 | 256 | 0.60 | 0.80 | 21 | empty |
| 4 | 234 | 0.56 | 0.79 | 19 | empty |
| 5 | 299 | 0.56 | 0.76 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–D · 729 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–F · 703 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 580 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- E–F · 568 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- B–E · 541 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4NRW · MvNei1-G86D · 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 Q5UQ00
- Elsewhere: RCSB PDB 4NRW · PDBe 4NRW · UniProt Q5UQ00
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