MolNFT v1 · #92798 · protein
Crystal structure of pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with L-rhamnopyranose
4GJI: “Crystal structure of pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with L-rhamnopyranose”. X-ray diffraction, 4 ligands (RNS, RM4, RAM), 20 pockets (best druggability 0.82). MolNFT v1 #92798 on GenesisL1: 3D…
- PDB
- 4GJI
- Type
- protein
- Length
- 1,688 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
- RNS, RM4, RAM, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-rhamnose isomerase (EC 5.3.1.14) | protein | 421 | 50% helix, 10% strand | Q75WH8 |
| C | L-rhamnose isomerase (EC 5.3.1.14) | protein | 427 | 49% helix, 11% strand | Q75WH8 |
| D | L-rhamnose isomerase (EC 5.3.1.14) | protein | 419 | 51% helix, 11% strand | Q75WH8 |
Ligands and binding sites
- RNS · L-rhamnose · ligand · 4 copies · chains A, B, C, D
- RM4 · beta-L-rhamnopyranose · ligand · 3 copies · chains A, B, C, D
- RAM · alpha-L-rhamnopyranose · sugar · 4 copies · chains A, C, B, D
- MN · Manganese (II) ion · metal · 10 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 | 210 | 0.82 | 0.95 | 49 | MN |
| 2 | 217 | 0.81 | 0.95 | 53 | MN |
| 3 | 963 | 0.81 | 0.83 | 77 | empty |
| 4 | 1053 | 0.81 | 0.83 | 86 | empty |
| 5 | 149 | 0.81 | 0.98 | 35 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2510 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 2458 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2153 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1982 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1697 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4GJI · Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant H101N 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 4GJI · PDBe 4GJI · UniProt Q75WH8
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