Research workbench
Metallo beta-lactamase fold protein (camp bound)
Analyse Metallo beta-lactamase fold protein (camp bound) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E3W
- Type
- protein
- Length
- 1,401 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0173 metal-dependent hydrolase C7P97_11315
- UniProt
- W8UA39
- Ligands
- CMP, ZN, NI, CL
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0173 metal-dependent hydrolase C7P97_11315 | protein | 238 | 21% helix, 29% strand | W8UA39 |
| B | UPF0173 metal-dependent hydrolase C7P97_11315 | protein | 239 | 21% helix, 28% strand | W8UA39 |
| C | UPF0173 metal-dependent hydrolase C7P97_11315 | protein | 230 | 23% helix, 30% strand | W8UA39 |
| D | UPF0173 metal-dependent hydrolase C7P97_11315 | protein | 232 | 22% helix, 29% strand | W8UA39 |
| E, F | UPF0173 metal-dependent hydrolase C7P97_11315 | protein | 231 | 22% helix, 30% strand | W8UA39 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- NI · Nickel (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.66 | 0.78 | 56 | TRS |
| 2 | 141 | 0.52 | 0.80 | 26 | CMP |
| 3 | 123 | 0.52 | 0.81 | 23 | empty |
| 4 | 166 | 0.51 | 0.78 | 26 | CMP |
| 5 | 136 | 0.51 | 0.80 | 26 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1109 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1104 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1102 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1100 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1094 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7E3W · Metallo beta-lactamase fold protein (cAMP bound) · the same entry in another collection · chain F against F, 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 W8UA39
- Elsewhere: RCSB PDB 7E3W · PDBe 7E3W · UniProt W8UA39
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