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Crystal structure of S. aureus tarm G117R mutant in complex with fondaparinux, alpha-glcnac-glycerol and udp

Analyse Crystal structure of S. aureus tarm G117R mutant in complex with fondaparinux… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X7R
Type: protein
Length: 986 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tarm
UniProt: H0AM96
Ligands: ZDO, SUS, UDP, 3YW, IDS, BDP, SGN
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tarm	protein	493	35% helix, 26% strand	H0AM96

Ligands and binding sites

ZDO · methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside · ligand · 2 copies · chains A, B
SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
3YW · (2S)-2,3-dihydroxypropyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside · ligand · 2 copies · chains A, B
IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 2 copies · chains A, B
BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A, B

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

Pockets

6 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	634	0.79	0.84	72	SGN, UDP, 3YW
2	638	0.79	0.84	73	SGN, UDP, 3YW
3	130	0.43	0.76	27	empty
4	196	0.43	0.73	22	empty
5	60	0.39	0.80	15	empty

Interfaces

1 interface between chains.

A–B · 93 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4X7R · Crystal structure of S. aureus TarM G117R mutant in complex with Fondaparinux… · 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 H0AM96
Elsewhere: RCSB PDB 4X7R · PDBe 4X7R · UniProt H0AM96

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