Research workbench
CAB2 mutant H337A complex with phosphopantothenoyl-cmp
Analyse CAB2 mutant H337A complex with phosphopantothenoyl-cmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AIK
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantothenate--cysteine ligase CAB2
- EC
- 6.3.2.5
- UniProt
- P40506
- Ligands
- PMT
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantothenate--cysteine ligase CAB2 (EC 6.3.2.5) | protein | 310 | 41% helix, 25% strand | P40506 |
| B | Phosphopantothenate--cysteine ligase CAB2 (EC 6.3.2.5) | protein | 308 | 40% helix, 25% strand | P40506 |
Ligands and binding sites
- PMT · Phosphoric acid mono-[3-(3-{[5-(4-amino-2-oxo-2H-pyrimidin-1-yl)-3,4- dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy-phosphoryloxy}-3-oxo-propylcarbamoyl)-3-hydroxy-2,2- dimethyl-propyl] ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.82 | 0.83 | 108 | empty |
| 2 | 630 | 0.82 | 0.86 | 61 | PMT |
| 3 | 613 | 0.81 | 0.86 | 53 | PMT |
| 4 | 56 | 0.28 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 2865 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 6AIK · Cab2 mutant H337A complex with phosphopantothenoyl-CMP · the same entry in another collection · chain A against A, TM-score 1.00
- P40506 · AlphaFold monomer V2.0 prediction for phosphopantothenate--cysteine ligase CAB2 (P40506) · a predicted model of the same protein · chain B 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 P40506
- Elsewhere: RCSB PDB 6AIK · PDBe 6AIK · UniProt P40506
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