Research workbench
Crystal structure of mltf from pseudomonas aeruginosa in complex with nam-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
- 5AA2
- Type
- protein
- Length
- 1,670 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 0.80
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 419 | 49% helix, 17% strand | Q9HXN1 |
| B | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 413 | 49% helix, 16% strand | Q9HXN1 |
| C | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 418 | 48% helix, 16% strand | Q9HXN1 |
| D | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 416 | 45% 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 · 2 copies · chains A, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.80 | 0.89 | 45 | empty |
| 2 | 314 | 0.79 | 0.90 | 43 | empty |
| 3 | 740 | 0.79 | 0.83 | 54 | empty |
| 4 | 768 | 0.77 | 0.81 | 56 | empty |
| 5 | 825 | 0.74 | 0.79 | 105 | empty |
Interfaces
4 interfaces between chains.
- A–C · 820 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 790 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 431 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 430 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 d-amino (covalent ligand, D-amino acid).
Compared structures
- 5AA2 · Crystal structure of MltF from Pseudomonas aeruginosa in complex with NAM-pentapeptide. · the same entry in another collection · chain E against E, TM-score 1.00
- Q9HXN1 · AlphaFold monomer V2.0 prediction for membrane-bound lytic murein transglycosylase F… · a predicted model of the same protein · chain C 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 5AA2 · PDBe 5AA2 · UniProt Q9HXN1
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