Research workbench
Crystal structure of the cbs pair of a putative D-arabinose 5- phosphate isomerase from methylococcus capsulatus in complex with cmp-kdo
Analyse Crystal structure of the cbs pair of a putative D-arabinose 5- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O9K
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arabinose 5-phosphate isomerase
- EC
- 5.3.1.13
- UniProt
- Q60AU8
- Ligands
- CMK
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arabinose 5-phosphate isomerase (EC 5.3.1.13) | protein | 130 | 35% helix, 28% strand | Q60AU8 |
| B | Arabinose 5-phosphate isomerase (EC 5.3.1.13) | protein | 128 | 36% helix, 29% strand | Q60AU8 |
Ligands and binding sites
- CMK · Cytidine 5'-monophosphate 3-deoxy-beta-D-gulo-oct-2-ulo-pyranosonic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.69 | 0.80 | 55 | CMK |
Interfaces
1 interface between chains.
- A–B · 1271 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4O9K · Crystal structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from… · 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 Q60AU8
- Elsewhere: RCSB PDB 4O9K · PDBe 4O9K · UniProt Q60AU8
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