MolNFT v1 · #54676 · protein

Crystal structure of sortase C-1 from actinomyces oris (formerly actinomyces naeslundii)

2XWG: “Crystal structure of sortase C-1 from actinomyces oris (formerly actinomyces naeslundii)”. X-ray diffraction, 1 ligand (CA), 11 pockets (best druggability 0.72). MolNFT v1 #54676 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2XWG
Type: protein
Length: 903 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sortase
UniProt: Q0Z952
Ligands: CA
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 19% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sortase	protein	181	21% helix, 32% strand	Q0Z952
B	Sortase	protein	185	22% helix, 31% strand	Q0Z952
C	Sortase	protein	176	18% helix, 32% strand	Q0Z952
D	Sortase	protein	184	20% helix, 31% strand	Q0Z952
E	Sortase	protein	177	16% helix, 33% strand	Q0Z952

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B, C

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

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	541	0.72	0.81	54	empty
2	397	0.65	0.79	34	empty
3	411	0.64	0.78	34	empty
4	311	0.59	0.78	28	empty
5	183	0.55	0.79	33	CA

Interfaces

4 interfaces between chains.

A–B · 749 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 705 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 637 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 488 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2XWG · Crystal structure of sortase C-1 from Actinomyces oris (formerly Actinomyces naeslundii) · 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 Q0Z952
Elsewhere: RCSB PDB 2XWG · PDBe 2XWG · UniProt Q0Z952

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