MolNFT v1 · #80989 · protein
Crystal structure of apo PBP1A from acinetobacter baumannii
3UDF · Penicillin-binding protein 1A: “Crystal structure of apo PBP1A from acinetobacter baumannii”. X-ray diffraction, 17 pockets (best druggability 0.73). MolNFT v1 #80989 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UDF
- Type
- protein
- Length
- 1,195 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1A
- UniProt
- G1C794
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1A | protein | 596 | 36% helix, 20% strand | G1C794 |
| B | Penicillin-binding protein 1A | protein | 599 | 37% helix, 19% strand | G1C794 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.73 | 0.84 | 43 | empty |
| 2 | 426 | 0.70 | 0.81 | 44 | empty |
| 3 | 247 | 0.53 | 0.76 | 43 | empty |
| 4 | 157 | 0.49 | 0.78 | 28 | empty |
| 5 | 186 | 0.48 | 0.76 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 2464 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3UDF · Crystal structure of Apo PBP1a from Acinetobacter baumannii · 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 G1C794
- Elsewhere: RCSB PDB 3UDF · PDBe 3UDF · UniProt G1C794
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