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Crystal structure of the streptococcus agalactiae sortase a

Analyse Crystal structure of the streptococcus agalactiae sortase a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RCC
Type: protein
Length: 2,341 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sortase srta
UniProt: Q8DZY1
Ligands: ZN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 16 distinct chains · 9% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sortase srta	protein	129	9% helix, 36% strand	Q8DZY1
B	Sortase srta	protein	124	10% helix, 42% strand	Q8DZY1
C	Sortase srta	protein	129	5% helix, 43% strand	Q8DZY1
D	Sortase srta	protein	129	10% helix, 40% strand	Q8DZY1
E	Sortase srta	protein	134	10% helix, 40% strand	Q8DZY1
F, G, P	Sortase srta	protein	132	10% helix, 47% strand	Q8DZY1
H	Sortase srta	protein	130	10% helix, 39% strand	Q8DZY1
I	Sortase srta	protein	131	10% helix, 40% strand	Q8DZY1
J	Sortase srta	protein	129	9% helix, 40% strand	Q8DZY1
K	Sortase srta	protein	129	10% helix, 44% strand	Q8DZY1
L	Sortase srta	protein	127	7% helix, 42% strand	Q8DZY1
M	Sortase srta	protein	128	9% helix, 41% strand	Q8DZY1
N	Sortase srta	protein	137	9% helix, 39% strand	Q8DZY1
O	Sortase srta	protein	131	9% helix, 44% strand	Q8DZY1
Q	Sortase srta	protein	133	10% helix, 41% strand	Q8DZY1
R	Sortase srta	protein	125	10% helix, 36% strand	Q8DZY1

Ligands and binding sites

ZN · Zinc ion · metal · 73 copies · chains A, B, L, C, K, D, J, E, I, F, H, G, M, N, R, O, P, Q

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	777	0.86	0.89	103	ZN
2	724	0.85	0.89	95	ZN
3	596	0.85	0.90	96	ZN
4	563	0.84	0.90	66	ZN
5	513	0.83	0.89	61	ZN

Interfaces

31 interfaces between chains.

B–K · 777 Å² buried · 15 hydrogen bonds · protein-protein
D–I · 756 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 750 Å² buried · 15 hydrogen bonds · protein-protein
A–L · 723 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 720 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3RCC · Crystal Structure of the Streptococcus agalactiae Sortase A · 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 Q8DZY1
Elsewhere: RCSB PDB 3RCC · PDBe 3RCC · UniProt Q8DZY1

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