MolNFT v1 · #171159 · protein

Crystal structure of the small alarmone hydrolase (sah) of pseudomonas aeruginosa

6YVC · Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'…: “Crystal structure of the small alarmone hydrolase (sah) of pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.77). MolNFT v1 #171159 on…

PDB: 6YVC
Type: protein
Length: 695 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase
UniProt: A0A071L0I0
Ligands: MN
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 72% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase	protein	175	71% helix, 2% strand	A0A071L0I0
B	Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase	protein	173	72% helix, 2% strand	A0A071L0I0
C	Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase	protein	175	71% helix, 2% strand	A0A071L0I0
D	Bifunctional (P)PPGPP SYNTHETASE/GUANOSINE-3',5'- BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase	protein	172	73% helix, 2% strand	A0A071L0I0

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

5 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	642	0.77	0.82	72	MN
2	517	0.69	0.79	44	MN
3	366	0.65	0.80	37	MN
4	254	0.61	0.80	31	empty
5	196	0.52	0.78	33	empty

Interfaces

5 interfaces between chains.

A–B · 1401 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 685 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 292 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 289 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 48 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6YVC · Crystal structure of the small alarmone hydrolase (SAH) of Pseudomonas aeruginosa · 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 A0A071L0I0
Elsewhere: RCSB PDB 6YVC · PDBe 6YVC · UniProt A0A071L0I0

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