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Crystal structure of MutM from Neisseria meningitidis
Analyse Crystal structure of MutM from Neisseria meningitidis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TC9
- Type
- protein + DNA
- Length
- 570 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.175
- Source
- Neisseria meningitidis alpha522; SYNTHETIC CONSTRUCT
- Molecule
- DNA containing abasic site analogue; Formamidopyrimidine-DNA glycosylase; DNA
- EC
- 3.2.2.23, 4.2.99.18
- UniProt
- I4E596
- Ligands
- ZN, MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.175 · 4 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, G | DNA containing abasic site analogue | dna | 12 | — | — |
| A | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 259 | 28% helix, 23% strand | I4E596 |
| B, F | DNA | dna | 14 | — | — |
| C | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 259 | 27% helix, 24% strand | I4E596 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.71 | 0.78 | 45 | empty |
| 2 | 666 | 0.71 | 0.78 | 46 | empty |
| 3 | 439 | 0.69 | 0.80 | 44 | MG |
| 4 | 266 | 0.46 | 0.72 | 30 | empty |
| 5 | 175 | 0.41 | 0.73 | 20 | empty |
Interfaces
7 interfaces between chains.
- G–C · 744 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–A · 741 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 733 Ų buried · 4 hydrogen bonds · protein-protein
- D–B · 529 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- G–F · 528 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6TC9 · Crystal structure of mutm from neisseria meningitidis · 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 I4E596
- Elsewhere: RCSB PDB 6TC9 · PDBe 6TC9 · UniProt I4E596
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