Research workbench
Crystal structure I of murf from acinetobacter baumannii
Analyse Crystal structure I of murf from acinetobacter baumannii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QF5
- Type
- protein
- Length
- 912 residues
- Chains
- 2
- 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
- B7GVN5
- Ligands
- ATP, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 459 | 39% helix, 23% strand | B7GVN5 |
| B | Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (EC 6.3.2.10) | protein | 453 | 39% helix, 23% strand | B7GVN5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.74 | 0.81 | 78 | ATP, MG |
| 2 | 644 | 0.74 | 0.81 | 83 | ATP, MG |
| 3 | 721 | 0.67 | 0.76 | 67 | empty |
| 4 | 110 | 0.47 | 0.79 | 19 | empty |
| 5 | 93 | 0.42 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 178 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4QF5 · Crystal structure I of MurF 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 B7GVN5
- Elsewhere: RCSB PDB 4QF5 · PDBe 4QF5 · UniProt B7GVN5
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