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VCA0105 paar-repeat protein from vibrio cholerae in complex with a vgrg-like beta-helix that is based on a fragment of T4 GP5

Analyse VCA0105 paar-repeat protein from vibrio cholerae in complex with a vgrg-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JIV
Type: protein
Length: 372 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tail-associated lysozyme; Putative uncharacterized protein
EC: 3.2.1.17
UniProt: P16009, Q9KN60
Ligands: PLM, STE, ELA, MG, ZN
Pockets: 1 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Tail-associated lysozyme (EC 3.2.1.17)	protein	93	0% helix, 65% strand	P16009
D	Putative uncharacterized protein	protein	93	0% helix, 49% strand	Q9KN60

Ligands and binding sites

PLM · Palmitic acid · ligand · chains A, B, C
STE · Stearic acid · ligand · chains A, B, C
ELA · 9-octadecenoic acid · ligand · chains A, B, C
MG · Magnesium ion · metal · chains A, B, C
ZN · Zinc ion · metal · chains D

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1092	0.84	0.85	72	PLM, STE, ELA

Interfaces

6 interfaces between chains.

B–C · 3801 Å² buried · 110 hydrogen bonds · protein-protein
A–B · 3763 Å² buried · 107 hydrogen bonds · protein-protein
A–C · 3724 Å² buried · 107 hydrogen bonds · protein-protein
C–D · 282 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 282 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4JIV · VCA0105 PAAR-repeat protein from Vibrio cholerae in complex with a VgrG-like beta-helix… · the same entry in another collection · chain A against A, TM-score 1.00

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 P16009
Every structure of UniProt Q9KN60
Elsewhere: RCSB PDB 4JIV · PDBe 4JIV · UniProt P16009 · UniProt Q9KN60

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