MolNFT v1 · #146169 · protein
T4-lysozyme fusion to geobacter ggdef
6D9M · Fusion protein of ENDOLYSIN,RESPONSE receiver sensor…: “T4-lysozyme fusion to geobacter ggdef”. X-ray diffraction, 4 ligands (GTP, GMP, POP), 4 pockets (best druggability 0.60). MolNFT v1 #146169 on GenesisL1: 3D structure, binding…
- PDB
- 6D9M
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion protein of ENDOLYSIN,RESPONSE receiver sensor diguanylate cyclase, gaf…
- EC
- 3.2.1.17
- UniProt
- D9IEF7, Q39UD1
- Ligands
- GTP, GMP, POP, MG
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion protein of ENDOLYSIN,RESPONSE receiver sensor diguanylate cyclase, gaf domain-containing (EC 3.2.1.17) | protein | 326 | 56% helix, 16% strand | D9IEF7, Q39UD1 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A
- GMP · Guanosine · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.60 | 0.76 | 34 | GTP, ACT |
| 2 | 77 | 0.47 | 0.82 | 15 | empty |
| 3 | 54 | 0.38 | 0.80 | 19 | empty |
| 4 | 56 | 0.33 | 0.77 | 18 | GTP |
Compared structures
- 6D9M · T4-Lysozyme fusion to Geobacter GGDEF · 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 D9IEF7
- Every structure of UniProt Q39UD1
- Elsewhere: RCSB PDB 6D9M · PDBe 6D9M · UniProt D9IEF7 · UniProt Q39UD1
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