Research workbench
Acinetobacter baumannii undecaprenyl pyrophosphate synthase (ab-upps) in complex with GW197
Analyse Acinetobacter baumannii undecaprenyl pyrophosphate synthase (ab-upps) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SZH
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)- farnesyl-diphosphate specific)
- EC
- 2.5.1.31
- UniProt
- V5VCK8
- Ligands
- M2H, CA
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)- farnesyl-diphosphate specific) (EC 2.5.1.31) | protein | 226 | 49% helix, 16% strand | V5VCK8 |
| B | DITRANS,POLYCIS-undecaprenyl-diphosphate synthase ((2E,6E)- farnesyl-diphosphate specific) (EC 2.5.1.31) | protein | 213 | 44% helix, 16% strand | V5VCK8 |
Ligands and binding sites
- M2H · 3,5-dimethyl-1~{H}-pyrrole-2-carbonitrile · ligand · chains A, B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.76 | 0.88 | 31 | empty |
| 2 | 64 | 0.75 | 0.99 | 21 | M2H |
| 3 | 395 | 0.65 | 0.79 | 35 | empty |
| 4 | 68 | 0.38 | 0.78 | 16 | empty |
| 5 | 53 | 0.32 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1606 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6SZH · Acinetobacter baumannii undecaprenyl pyrophosphate synthase (AB-UppS) in complex with… · 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 V5VCK8
- Elsewhere: RCSB PDB 6SZH · PDBe 6SZH · UniProt V5VCK8
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