Research workbench
Crystal structure of a trap periplasmic solute binding protein from desulfovibrio alaskensis G20 (DDE_0634), target efi-510102, with bound D-tryptophan
Analyse Crystal structure of a trap periplasmic solute binding protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NAP
- Type
- protein
- Length
- 1,236 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein, family 7
- UniProt
- Q315G1
- Ligands
- DTR
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular solute-binding protein, family 7 | protein | 308 | 49% helix, 19% strand | Q315G1 |
| B | Extracellular solute-binding protein, family 7 | protein | 309 | 51% helix, 19% strand | Q315G1 |
| C | Extracellular solute-binding protein, family 7 | protein | 309 | 51% helix, 19% strand | Q315G1 |
| D | Extracellular solute-binding protein, family 7 | protein | 310 | 51% helix, 18% strand | Q315G1 |
Ligands and binding sites
- DTR · D-tryptophan · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.81 | 0.83 | 138 | empty |
| 2 | 66 | 0.75 | 0.98 | 17 | DTR |
| 3 | 56 | 0.72 | 0.98 | 17 | DTR |
| 4 | 53 | 0.72 | 0.98 | 18 | DTR |
| 5 | 55 | 0.72 | 0.98 | 17 | DTR |
Interfaces
5 interfaces between chains.
- B–D · 720 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 522 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 449 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 160 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (engineered).
Compared structures
- 4NAP · Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio… · the same entry in another collection · chain B against B, TM-score 1.00
- Q315G1 · AlphaFold monomer V2.0 prediction for solute-binding protein DDE_0634 (Q315G1) · a predicted model of the same protein · chain D 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 Q315G1
- Elsewhere: RCSB PDB 4NAP · PDBe 4NAP · UniProt Q315G1
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