Research workbench
Crystal structure of a pduo-type ATP:COBALAMIN adenosyltransferase from burkholderia thailandensis
Analyse Crystal structure of a pduo-type ATP:COBALAMIN adenosyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZHZ
- Type
- protein
- Length
- 494 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP:COB(I)ALAMIN adenosyltransferase, putative
- EC
- 2.5.1.17
- UniProt
- Q2SZ09
- Ligands
- ATP, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP:COB(I)ALAMIN adenosyltransferase, putative (EC 2.5.1.17) | protein | 148 | 71% helix, 1% strand | Q2SZ09 |
| B | ATP:COB(I)ALAMIN adenosyltransferase, putative (EC 2.5.1.17) | protein | 174 | 61% helix, 6% strand | Q2SZ09 |
| C | ATP:COB(I)ALAMIN adenosyltransferase, putative (EC 2.5.1.17) | protein | 172 | 61% helix, 5% strand | Q2SZ09 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.69 | 0.97 | 16 | empty |
| 2 | 534 | 0.67 | 0.78 | 34 | GOL |
| 3 | 465 | 0.65 | 0.77 | 35 | MG, ATP |
| 4 | 419 | 0.64 | 0.78 | 34 | MG, ATP |
| 5 | 203 | 0.51 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1416 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1305 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 776 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2ZHZ · Crystal structure of a pduO-type ATP:cobalamin adenosyltransferase from Burkholderia… · 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 Q2SZ09
- Elsewhere: RCSB PDB 2ZHZ · PDBe 2ZHZ · UniProt Q2SZ09
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