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Crystal structure of ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE family protein from bacteroides thetaiotaomicron, northeast structural genomics consortium target BTR318A
Analyse Crystal structure of ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE family protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MPR
- Type
- protein
- Length
- 1,109 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE family protein
- UniProt
- Q8A183
- Ligands
- BR, UNL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE family protein | protein | 282 | 21% helix, 33% strand | Q8A183 |
| B | Putative ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE family protein | protein | 271 | 22% helix, 34% strand | Q8A183 |
| C | Putative ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE family protein | protein | 281 | 20% helix, 33% strand | Q8A183 |
| D | Putative ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE family protein | protein | 275 | 21% helix, 34% strand | Q8A183 |
Ligands and binding sites
- BR · Bromide ion · ion · 14 copies · chains A, D, B, C
- UNL · Unknown ligand · ion · 8 copies · chains A
- ACY · Acetic acid · additive · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.82 | 0.84 | 116 | BR, PEG |
| 2 | 484 | 0.74 | 0.83 | 45 | BR |
| 3 | 239 | 0.61 | 0.81 | 24 | empty |
| 4 | 239 | 0.57 | 0.78 | 35 | ACY, BR |
| 5 | 55 | 0.41 | 0.82 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1457 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 607 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 425 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 284 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3MPR · Crystal Structure of endonuclease/exonuclease/phosphatase family protein from Bacteroides… · 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 Q8A183
- Elsewhere: RCSB PDB 3MPR · PDBe 3MPR · UniProt Q8A183
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