MolNFT v1 · #109254 · protein + DNA
Crystal structure of mycobacterium tuberculosis ogt in complex with DNA
4WX9 · DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3'): “Crystal structure of mycobacterium tuberculosis ogt in complex with DNA”. X-ray diffraction, 8 pockets (best druggability 0.51). MolNFT v1 #109254 on GenesisL1: 3D…
- PDB
- 4WX9
- Type
- protein + DNA
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3'); DNA…
- EC
- 2.1.1.63
- UniProt
- P9WJW5
- Pockets
- 8 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3') | dna | 13 | — | — |
| E | DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3') | dna | 13 | — | — |
| A | Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) | protein | 161 | 37% helix, 17% strand | P9WJW5 |
| B, C | Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) | protein | 164 | 35% helix, 16% strand | P9WJW5 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.51 | 0.75 | 45 | empty |
| 2 | 114 | 0.42 | 0.77 | 26 | empty |
| 3 | 117 | 0.41 | 0.77 | 15 | empty |
| 4 | 63 | 0.40 | 0.80 | 17 | empty |
| 5 | 65 | 0.35 | 0.77 | 17 | empty |
Interfaces
5 interfaces between chains.
- D–A · 592 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–E · 515 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- E–A · 310 Ų buried · 1 hydrogen bond · protein-nucleic
- A–B · 65 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4WX9 · Crystal structure of Mycobacterium tuberculosis OGT in complex with DNA · the same entry in another collection · chain E against E, TM-score 1.00
- P9WJW5 · AlphaFold monomer V2.0 prediction for methylated-DNA--protein- cysteine methyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P9WJW5
- Elsewhere: RCSB PDB 4WX9 · PDBe 4WX9 · UniProt P9WJW5
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