MolNFT v1 · #78354 · protein

The crystal structure of a hydrolase from pseudomonas syringae

3S6J · Hydrolase, haloacid dehalogenase-like family: “The crystal structure of a hydrolase from pseudomonas syringae”. X-ray diffraction, 1 ligand (CA), 19 pockets (best druggability 0.64). MolNFT v1 #78354 on GenesisL1: 3D structure…

PDB: 3S6J
Type: protein
Length: 1,292 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydrolase, haloacid dehalogenase-like family
UniProt: Q88AV7
Ligands: CA
Pockets: 19 · best druggability 0.64

Structure

x-ray diffraction · 6 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hydrolase, haloacid dehalogenase-like family	protein	216	52% helix, 13% strand	Q88AV7
B	Hydrolase, haloacid dehalogenase-like family	protein	209	48% helix, 13% strand	Q88AV7
C	Hydrolase, haloacid dehalogenase-like family	protein	212	48% helix, 13% strand	Q88AV7
D	Hydrolase, haloacid dehalogenase-like family	protein	216	52% helix, 14% strand	Q88AV7
E	Hydrolase, haloacid dehalogenase-like family	protein	220	55% helix, 13% strand	Q88AV7
F	Hydrolase, haloacid dehalogenase-like family	protein	219	53% helix, 13% strand	Q88AV7

Ligands and binding sites

CA · Calcium ion · metal · 9 copies · chains A, B, F, C, D, E

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

Pockets

19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	270	0.64	0.81	39	CA
2	502	0.63	0.76	55	empty
3	177	0.62	0.84	34	CA
4	168	0.61	0.84	33	empty
5	255	0.61	0.80	44	CA

Interfaces

8 interfaces between chains.

C–D · 954 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 941 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 933 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 199 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 190 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 modified (engineered).

Compared structures

3S6J · The crystal structure of a hydrolase from Pseudomonas syringae · 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 Q88AV7
Elsewhere: RCSB PDB 3S6J · PDBe 3S6J · UniProt Q88AV7

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