MolNFT v1 · #67755 · protein
Crystal structure of pseudomonas stutzeri L-rhamnose isomerase mutant S329K in complex with D-psicose
3ITV: “Crystal structure of pseudomonas stutzeri L-rhamnose isomerase mutant S329K in complex with D-psicose”. X-ray diffraction, 2 ligands (PSJ, MN), 20 pockets (best druggability 0.88). MolNFT v1 #67755 on GenesisL1: 3D structure…
- PDB
- 3ITV
- Type
- protein
- Length
- 1,685 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-rhamnose isomerase
- EC
- 5.3.1.14
- UniProt
- Q75WH8
- Ligands
- PSJ, MN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-rhamnose isomerase (EC 5.3.1.14) | protein | 421 | 50% helix, 11% strand | Q75WH8 |
| B | L-rhamnose isomerase (EC 5.3.1.14) | protein | 420 | 50% helix, 12% strand | Q75WH8 |
| C | L-rhamnose isomerase (EC 5.3.1.14) | protein | 426 | 49% helix, 11% strand | Q75WH8 |
| D | L-rhamnose isomerase (EC 5.3.1.14) | protein | 418 | 50% helix, 11% strand | Q75WH8 |
Ligands and binding sites
- PSJ · D-psicose · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.88 | 0.95 | 97 | empty |
| 2 | 1011 | 0.83 | 0.84 | 97 | empty |
| 3 | 1027 | 0.83 | 0.84 | 104 | empty |
| 4 | 146 | 0.81 | 0.98 | 35 | empty |
| 5 | 143 | 0.80 | 0.97 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2488 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 2399 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2085 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1983 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1713 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3ITV · Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant S329K in complex… · 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 Q75WH8
- Elsewhere: RCSB PDB 3ITV · PDBe 3ITV · UniProt Q75WH8
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