Research workbench
Crystal structure of mltf from pseudomonas aeruginosa in complex with nag-anhnam-pentapeptide
Analyse Crystal structure of mltf from pseudomonas aeruginosa in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AA1
- Type
- protein
- Length
- 1,671 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-bound lytic murein transglycosylase F…
- EC
- 4.2.2.-
- UniProt
- Q9HXN1
- Ligands
- AH0, API, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 418 | 47% helix, 15% strand | Q9HXN1 |
| B | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 413 | 46% helix, 14% strand | Q9HXN1 |
| C | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 419 | 45% helix, 16% strand | Q9HXN1 |
| D | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 417 | 46% helix, 16% strand | Q9HXN1 |
| E | N-acetylglucosamine-1,6-anhydro-N-acetylmuramic acid L-ala- D-glu-M-dap-D-ala-D-ala | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- AH0 · 2-(2-acetylamino-4-hydroxy-6,8-dioxa-bicyclo[3.2.1]oct-3-yloxy)-propionic acid · ligand · chains A, E
- API · 2,6-diaminopimelic acid · ligand · chains A, E
- CL · Chloride ion · ion · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.84 | 0.91 | 38 | empty |
| 2 | 789 | 0.80 | 0.83 | 61 | empty |
| 3 | 416 | 0.78 | 0.87 | 43 | empty |
| 4 | 892 | 0.76 | 0.79 | 55 | empty |
| 5 | 829 | 0.72 | 0.77 | 77 | empty |
Interfaces
6 interfaces between chains.
- B–D · 828 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 696 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 425 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 361 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 2 d-amino, 1 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- Q9HXN1 · AlphaFold monomer V2.0 prediction for membrane-bound lytic murein transglycosylase F… · a predicted model of the same protein · chain B against A, TM-score 0.66
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 Q9HXN1
- Elsewhere: RCSB PDB 5AA1 · PDBe 5AA1 · UniProt Q9HXN1
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