MolNFT v1 · #142884 · protein
CAB2 mutant-H337A complex with phosphopantothenoylcystine
6AIP · Phosphopantothenate--cysteine ligase CAB2: “CAB2 mutant-H337A complex with phosphopantothenoylcystine”. X-ray diffraction, 1 ligand (9Z6), 5 pockets (best druggability 0.83). MolNFT v1 #142884 on GenesisL1: 3D structure, binding…
- PDB
- 6AIP
- Type
- protein
- Length
- 620 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
- 9Z6
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphopantothenate--cysteine ligase CAB2 (EC 6.3.2.5) | protein | 310 | 40% helix, 23% strand | P40506 |
Ligands and binding sites
- 9Z6 · (5R,12R,17R)-17-amino-12-carboxy-1,1,5-trihydroxy-4,4-dimethyl-6,10-dioxo-2-oxa-14,15-dithia-7,11-diaza-1-phosphaoctadecan-18-oic acid 1-oxide (non-preferred name) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.83 | 0.89 | 58 | 9Z6 |
| 2 | 544 | 0.82 | 0.88 | 53 | 9Z6 |
| 3 | 580 | 0.75 | 0.81 | 57 | empty |
| 4 | 527 | 0.74 | 0.82 | 79 | empty |
| 5 | 122 | 0.55 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2915 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6AIP · Cab2 mutant-H337A complex with phosphopantothenoylcystine · 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 0.99
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 6AIP · PDBe 6AIP · UniProt P40506
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