Research workbench
Crystal structure of a putative racemase with mg ion
Analyse Crystal structure of a putative racemase with mg ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NZG
- Type
- protein
- Length
- 1,511 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative racemase
- UniProt
- B6R2Z6
- Ligands
- MG
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative racemase | protein | 377 | 40% helix, 17% strand | B6R2Z6 |
| D | Putative racemase | protein | 380 | 41% helix, 17% strand | B6R2Z6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, C, B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.88 | 0.89 | 162 | MG |
| 2 | 153 | 0.79 | 0.95 | 26 | empty |
| 3 | 515 | 0.72 | 0.81 | 40 | GOL |
| 4 | 557 | 0.72 | 0.80 | 46 | GOL |
| 5 | 549 | 0.71 | 0.79 | 44 | GOL |
Interfaces
5 interfaces between chains.
- B–D · 1760 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1757 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1135 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 477 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3NZG · Crystal structure of a putative racemase with Mg ion · 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 B6R2Z6
- Elsewhere: RCSB PDB 3NZG · PDBe 3NZG · UniProt B6R2Z6
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