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Crystal structure of ompa peptidoglycan-binding domain from acinetobacter baumannii

Analyse Crystal structure of ompa peptidoglycan-binding domain from acinetobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1010 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 896 Å² buried · 20 hydrogen bonds · protein-protein
E–H · 887 Å² buried · 22 hydrogen bonds · protein-protein
A–G · 369 Å² 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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