MolNFT v1 · #92443 · protein
Crystal structure of ompa peptidoglycan-binding domain from acinetobacter baumannii
4G88 · Outer membrane protein OMP38: “Crystal structure of ompa peptidoglycan-binding domain from acinetobacter baumannii”. X-ray diffraction, 2 ligands (API, SRT), 5 pockets (best druggability 0.61). MolNFT v1 #92443 on GenesisL1: 3D…
- PDB
- 4G88
- Type
- protein
- Length
- 973 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein OMP38
- UniProt
- Q6RYW5
- Ligands
- API, SRT
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Outer membrane protein OMP38 | protein | 122 | 39% helix, 28% strand | Q6RYW5 |
| C, E | Outer membrane protein OMP38 | protein | 120 | 41% helix, 28% strand | Q6RYW5 |
| D, G | Outer membrane protein OMP38 | protein | 123 | 39% helix, 28% strand | Q6RYW5 |
| H | Outer membrane protein OMP38 | protein | 121 | 40% helix, 28% strand | Q6RYW5 |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · 8 copies · chains A, E, B, C, D, F, G, H
- SRT · S,R meso-tartaric acid · ligand · 2 copies · chains D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.61 | 0.75 | 54 | API |
| 2 | 272 | 0.54 | 0.76 | 42 | empty |
| 3 | 120 | 0.52 | 0.82 | 28 | empty |
| 4 | 96 | 0.34 | 0.74 | 20 | empty |
| 5 | 80 | 0.31 | 0.74 | 21 | empty |
Interfaces
12 interfaces between chains.
- F–G · 1019 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1010 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 20 hydrogen bonds · protein-protein
- E–H · 887 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 369 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4G88 · Crystal structure of OmpA peptidoglycan-binding domain from Acinetobacter baumannii · the same entry in another collection · chain H against H, TM-score 1.00
- Q6RYW5 · AlphaFold monomer V2.0 prediction for outer membrane protein OMP38 (Q6RYW5) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q6RYW5
- Elsewhere: RCSB PDB 4G88 · PDBe 4G88 · UniProt Q6RYW5
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