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Crystal structure of a putative metallo-beta-lactamase (TM0894) from thermotoga maritima at 2.10 a resolution
Analyse Crystal structure of a putative metallo-beta-lactamase (TM0894) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZTC
- Type
- protein
- Length
- 833 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TM0894
- UniProt
- Q9WZZ6
- Ligands
- NI, PO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein TM0894 | protein | 209 | 33% helix, 29% strand | Q9WZZ6 |
| C | Hypothetical protein TM0894 | protein | 207 | 33% helix, 29% strand | Q9WZZ6 |
| D | Hypothetical protein TM0894 | protein | 208 | 33% helix, 30% strand | Q9WZZ6 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, D, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.83 | 0.84 | 81 | empty |
| 2 | 1104 | 0.83 | 0.84 | 80 | empty |
| 3 | 152 | 0.56 | 0.81 | 22 | PO4 |
| 4 | 172 | 0.55 | 0.80 | 21 | empty |
| 5 | 76 | 0.40 | 0.78 | 15 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1784 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1770 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 841 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 833 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 200 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1ZTC · Crystal structure of a putative metallo-beta-lactamase (tm0894) from Thermotoga maritima… · 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 Q9WZZ6
- Elsewhere: RCSB PDB 1ZTC · PDBe 1ZTC · UniProt Q9WZZ6
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