MolNFT v1 · #95533 · protein
Crystal structure of enolase PFL01_3283 (target efi-502286) from pseudomonas fluorescens PF0-1 with bound magnesium, potassium and tartrate
4IT1 · Putative glucarate dehydratase: “Crystal structure of enolase PFL01_3283 (target efi-502286) from pseudomonas fluorescens PF0-1 with bound…”. X-ray diffraction, 3 ligands (BCT, MG, K), 17 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 4IT1
- Type
- protein
- Length
- 1,704 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glucarate dehydratase
- UniProt
- Q3KB33
- Ligands
- BCT, MG, K
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative glucarate dehydratase | protein | 426 | 41% helix, 17% strand | Q3KB33 |
| B | Putative glucarate dehydratase | protein | 425 | 40% helix, 17% strand | Q3KB33 |
| D | Putative glucarate dehydratase | protein | 427 | 40% helix, 18% strand | Q3KB33 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- K · Potassium ion · metal · 2 copies · chains B, C
- TLA · L(+)-tartaric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.81 | 0.88 | 68 | TLA |
| 2 | 549 | 0.81 | 0.87 | 69 | TLA |
| 3 | 690 | 0.78 | 0.83 | 69 | BCT |
| 4 | 669 | 0.78 | 0.83 | 69 | empty |
| 5 | 63 | 0.72 | 0.98 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1319 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1315 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 574 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 541 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 473 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4IT1 · Crystal structure of enolase pfl01_3283 (target efi-502286) from pseudomonas fluorescens… · 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 Q3KB33
- Elsewhere: RCSB PDB 4IT1 · PDBe 4IT1 · UniProt Q3KB33
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