MolNFT v1 · #102899 · protein
Bacterial cellulose synthase in complex with cyclic-di-gmp and udp
4P00 · Cellulose synthase a subunit: “Bacterial cellulose synthase in complex with cyclic-di-gmp and udp”. X-ray diffraction, 6 ligands (C2E, UDP, PLC), 19 pockets (best druggability 0.90). MolNFT v1 #102899 on GenesisL1: 3D structure…
- PDB
- 4P00
- Type
- protein
- Length
- 1,392 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulose synthase a subunit; Cellulose synthase B subunit; Unidentified peptide
- EC
- 2.4.1.12
- UniProt
- Q3J125, Q3J126
- Ligands
- C2E, UDP, PLC, 3PE, BGC, MG
- Pockets
- 19 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulose synthase a subunit (EC 2.4.1.12) | protein | 728 | 51% helix, 12% strand | Q3J125 |
| B | Cellulose synthase B subunit | protein | 655 | 22% helix, 29% strand | Q3J126 |
| D | Unidentified peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A
- UDP · Uridine-5'-diphosphate · ligand · chains A
- PLC · Diundecyl phosphatidyl choline · ligand · chains A
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · 17 copies · chains B, A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.90 | 0.91 | 110 | BGC, UDP, MG |
| 2 | 393 | 0.82 | 0.90 | 53 | empty |
| 3 | 621 | 0.77 | 0.83 | 75 | empty |
| 4 | 460 | 0.74 | 0.82 | 41 | empty |
| 5 | 350 | 0.61 | 0.78 | 33 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2360 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 228 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4P00 · Bacterial Cellulose Synthase in complex with cyclic-di-GMP and UDP · 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 Q3J125
- Every structure of UniProt Q3J126
- Elsewhere: RCSB PDB 4P00 · PDBe 4P00 · UniProt Q3J125 · UniProt Q3J126
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