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Crystal structure of putative hydrolase (2632844) from bacillus subtilis at 1.96 a resolution
Analyse Crystal structure of putative hydrolase (2632844) from bacillus subtilis at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R11
- Type
- protein
- Length
- 1,143 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxylesterase np
- EC
- 3.1.1.1
- UniProt
- P96688
- Ligands
- MG, CL
- Pockets
- 9 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxylesterase np (EC 3.1.1.1) | protein | 283 | 41% helix, 18% strand | P96688 |
| B | Carboxylesterase np (EC 3.1.1.1) | protein | 287 | 40% helix, 19% strand | P96688 |
| C | Carboxylesterase np (EC 3.1.1.1) | protein | 285 | 43% helix, 18% strand | P96688 |
| D | Carboxylesterase np (EC 3.1.1.1) | protein | 288 | 40% helix, 19% strand | P96688 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.90 | 0.91 | 123 | PGE |
| 2 | 466 | 0.86 | 0.93 | 68 | EDO |
| 3 | 436 | 0.86 | 0.93 | 65 | empty |
| 4 | 474 | 0.64 | 0.77 | 46 | empty |
| 5 | 112 | 0.41 | 0.77 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1137 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1130 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 206 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 2R11 · Crystal structure of putative hydrolase (2632844) from Bacillus subtilis at 1.96 A… · the same entry in another collection · chain D against D, TM-score 1.00
- P96688 · AlphaFold monomer V2.0 prediction for uncharacterized carboxylesterase nap (P96688) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P96688
- Elsewhere: RCSB PDB 2R11 · PDBe 2R11 · UniProt P96688
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