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Ripd (RV1566C) from mycobacterium tuberculosis: a non-catalytic NLPC/P60 domain protein, adaptation to peptidoglycan-binding function

Analyse Ripd (RV1566C) from mycobacterium tuberculosis: a non-catalytic NLPC/P60 domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JXB
Type: protein
Length: 259 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Invasion-associated protein
UniProt: O06624
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Invasion-associated protein	protein	130	32% helix, 29% strand	O06624
B	Invasion-associated protein	protein	129	28% helix, 29% strand	O06624

Ligands and binding sites

ACT · Acetate ion · additive · 7 copies · chains A, B

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	229	0.50	0.75	27	ACT

Interfaces

1 interface between chains.

A–B · 444 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4JXB · RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein… · 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 O06624
Elsewhere: RCSB PDB 4JXB · PDBe 4JXB · UniProt O06624

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