MolNFT v1 · #62913 · protein
Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from bacteroides fragilis nctc 9343 at 1.70 a resolution
3ETN: “Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from…”. X-ray diffraction, 1 ligand (CMK), 7 pockets (best druggability 0.87). MolNFT v1 #62913 on GenesisL1: 3D structure, binding…
- PDB
- 3ETN
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphosugar isomerase involved in capsule formation
- UniProt
- Q5LIW1
- Ligands
- CMK
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative phosphosugar isomerase involved in capsule formation | protein | 192 | 53% helix, 13% strand | Q5LIW1 |
| B, D | Putative phosphosugar isomerase involved in capsule formation | protein | 198 | 52% helix, 12% strand | Q5LIW1 |
Ligands and binding sites
- CMK · Cytidine 5'-monophosphate 3-deoxy-beta-D-gulo-oct-2-ulo-pyranosonic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.87 | 0.88 | 59 | empty |
| 2 | 212 | 0.59 | 0.81 | 33 | CMK |
| 3 | 208 | 0.59 | 0.81 | 26 | CMK |
| 4 | 229 | 0.58 | 0.79 | 31 | EDO, CMK |
| 5 | 213 | 0.58 | 0.80 | 36 | CMK, EDO |
Interfaces
6 interfaces between chains.
- C–D · 2379 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2371 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1190 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1183 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 512 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3ETN · Crystal structure of putative phosphosugar isomerase involved in capsule formation… · the same entry in another collection · chain B against B, 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 Q5LIW1
- Elsewhere: RCSB PDB 3ETN · PDBe 3ETN · UniProt Q5LIW1
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