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Structure of udp-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate--D-alanyl-D-alanyl ligase from acinetobacter baumannii
Analyse Structure of udp-N-acetylmuramoylalanyl-D-glutamyl-2,6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZIY
- Type
- protein
- Length
- 446 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
- EC
- 6.3.2.10
- UniProt
- A0A0A2TK68
- Ligands
- ANP, MG
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (EC 6.3.2.10) | protein | 446 | 36% helix, 23% strand | A0A0A2TK68 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.68 | 0.78 | 64 | ANP, MG |
| 2 | 87 | 0.32 | 0.73 | 20 | empty |
Compared structures
- 4ZIY · Structure of UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl… · 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 A0A0A2TK68
- Elsewhere: RCSB PDB 4ZIY · PDBe 4ZIY · UniProt A0A0A2TK68
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