Research workbench

SAV0551

Analyse SAV0551 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XR2
Type: protein
Length: 2,306 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PROTEIN/NUCLEIC acid deglycase hcha
EC: 3.1.2.-, 3.5.1.124
UniProt: P64312
Ligands: LAC, ZN
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124)	protein	287	38% helix, 17% strand	P64312
B	PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124)	protein	286	36% helix, 17% strand	P64312
C, G	PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124)	protein	295	39% helix, 17% strand	P64312
D	PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124)	protein	284	36% helix, 17% strand	P64312
E	PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124)	protein	287	38% helix, 17% strand	P64312
F	PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124)	protein	283	36% helix, 17% strand	P64312
H	PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124)	protein	289	37% helix, 16% strand	P64312

Ligands and binding sites

LAC · Lactic acid · ligand · 2 copies · chains A, E
ZN · Zinc ion · metal · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1085	0.79	0.81	95	empty
2	878	0.76	0.79	82	empty
3	621	0.75	0.81	71	empty
4	472	0.73	0.82	54	empty
5	637	0.71	0.78	61	empty

Interfaces

17 interfaces between chains.

C–D · 1216 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1216 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1198 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1166 Å² buried · 22 hydrogen bonds · protein-protein
A–F · 406 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5XR2 · SAV0551 · the same entry in another collection · chain H against H, TM-score 1.00
P64312 · AlphaFold monomer V2.0 prediction for PROTEIN/NUCLEIC acid deglycase hcha (P64312) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P64312
Elsewhere: RCSB PDB 5XR2 · PDBe 5XR2 · UniProt P64312

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