MolNFT v1 · #142881 · protein
CAB2 mutant H337A complex with phosphopantothenate-cysteine
6AIM · Phosphopantothenate--cysteine ligase CAB2: “CAB2 mutant H337A complex with phosphopantothenate-cysteine”. X-ray diffraction, 1 ligand (9Z3), 4 pockets (best druggability 0.82). MolNFT v1 #142881 on GenesisL1: 3D structure, binding…
- PDB
- 6AIM
- Type
- protein
- Length
- 617 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
- 9Z3
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantothenate--cysteine ligase CAB2 (EC 6.3.2.5) | protein | 308 | 41% helix, 25% strand | P40506 |
| B | Phosphopantothenate--cysteine ligase CAB2 (EC 6.3.2.5) | protein | 309 | 41% helix, 23% strand | P40506 |
Ligands and binding sites
- 9Z3 · N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl-L-cysteine · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.82 | 0.87 | 54 | 9Z3 |
| 2 | 477 | 0.80 | 0.87 | 50 | 9Z3 |
| 3 | 879 | 0.76 | 0.79 | 73 | empty |
| 4 | 443 | 0.72 | 0.82 | 68 | empty |
Interfaces
1 interface between chains.
- A–B · 2955 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 6AIM · Cab2 mutant H337A complex with phosphopantothenate-cysteine · 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 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 P40506
- Elsewhere: RCSB PDB 6AIM · PDBe 6AIM · UniProt P40506
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