MolNFT v1 · #139603 · protein
Crystal structure of MSMEG3575 in complex with benzoguanamine
5XKR · CMP/DCMP deaminase, zinc-binding protein: “Crystal structure of MSMEG3575 in complex with benzoguanamine”. X-ray diffraction, 2 ligands (BZE, ZN), 6 pockets (best druggability 0.64). MolNFT v1 #139603 on GenesisL1: 3D structure…
- PDB
- 5XKR
- Type
- protein
- Length
- 632 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CMP/DCMP deaminase, zinc-binding protein
- UniProt
- A0QY90
- Ligands
- BZE, ZN
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | CMP/DCMP deaminase, zinc-binding protein | protein | 158 | 51% helix, 16% strand | A0QY90 |
Ligands and binding sites
- BZE · 6-phenyl-1,3,5-triazine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.64 | 0.87 | 27 | BZE, GOL |
| 2 | 167 | 0.63 | 0.84 | 29 | BZE, GOL |
| 3 | 146 | 0.62 | 0.85 | 31 | BZE, GOL |
| 4 | 143 | 0.61 | 0.84 | 27 | BZE, GOL |
| 5 | 70 | 0.34 | 0.76 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1139 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1136 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 462 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XKR · Crystal structure of Msmeg3575 in complex with benzoguanamine · 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 A0QY90
- Elsewhere: RCSB PDB 5XKR · PDBe 5XKR · UniProt A0QY90
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