Research workbench
Crystal structure of L-rhamnose isomerase from pseudomonas stutzeri with metal ion
Analyse Crystal structure of L-rhamnose isomerase from pseudomonas stutzeri with metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HCV
- Type
- protein
- Length
- 1,679 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
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 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, 10% strand | Q75WH8 |
| D | L-rhamnose isomerase (EC 5.3.1.14) | protein | 417 | 50% helix, 11% strand | Q75WH8 |
Ligands and binding sites
- ZN · Zinc 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 | 997 | 0.83 | 0.84 | 99 | empty |
| 2 | 1033 | 0.83 | 0.84 | 108 | empty |
| 3 | 195 | 0.82 | 0.96 | 43 | empty |
| 4 | 185 | 0.81 | 0.96 | 40 | empty |
| 5 | 136 | 0.80 | 0.98 | 35 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2508 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 2376 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2008 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1975 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1722 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2HCV · Crystal structure of L-rhamnose isomerase from Pseudomonas stutzeri with metal ion · the same entry in another collection · chain C against C, 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 2HCV · PDBe 2HCV · UniProt Q75WH8
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