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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: 4G4Z
Type: protein
Length: 968 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein OMP38
UniProt: Q6RYW5
Ligands: DAL, SO4
Pockets: 8 · best druggability 0.58

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Outer membrane protein OMP38	protein	120	40% helix, 28% strand	Q6RYW5
B, E, H	Outer membrane protein OMP38	protein	121	40% helix, 28% strand	Q6RYW5
C	Outer membrane protein OMP38	protein	119	41% helix, 27% strand	Q6RYW5
D, F, G	Outer membrane protein OMP38	protein	122	40% helix, 28% strand	Q6RYW5

Ligands and binding sites

DAL · D-alanine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	422	0.58	0.75	48	DAL
2	242	0.55	0.77	35	empty
3	78	0.46	0.82	15	empty
4	96	0.41	0.78	22	empty
5	57	0.39	0.81	12	empty

Interfaces

12 interfaces between chains.

F–G · 1032 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 958 Å² buried · 26 hydrogen bonds · protein-protein
E–H · 928 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 715 Å² buried · 17 hydrogen bonds · protein-protein
A–G · 378 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4G4Z · 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 0.99

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 4G4Z · PDBe 4G4Z · UniProt Q6RYW5

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