MolNFT v1 · #99542 · protein

Structure of the reduced, zn-bound form of mycobacterium tuberculosis peptidoglycan amidase RV3717

4M6I: “Structure of the reduced, zn-bound form of mycobacterium tuberculosis peptidoglycan amidase RV3717”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.56). MolNFT v1 #99542 on GenesisL1: 3D structure, binding sites…

PDB: 4M6I
Type: protein
Length: 359 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidoglycan amidase RV3717
EC: 3.5.-.-
UniProt: O69684
Ligands: ZN
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidoglycan amidase RV3717 (EC 3.5.-.-)	protein	185	43% helix, 22% strand	O69684
B	Peptidoglycan amidase RV3717 (EC 3.5.-.-)	protein	174	43% helix, 23% strand	O69684

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

3 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	154	0.56	0.81	29	empty
2	133	0.54	0.82	29	empty
3	103	0.42	0.77	21	empty

Interfaces

1 interface between chains.

A–B · 626 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4M6I · Structure of the reduced, Zn-bound form of Mycobacterium tuberculosis peptidoglycan… · 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 O69684
Elsewhere: RCSB PDB 4M6I · PDBe 4M6I · UniProt O69684

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