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Crystal structure of GDP-perosamine synthase

Analyse Crystal structure of GDP-perosamine synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BN1
Type: protein
Length: 1,465 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Perosamine synthetase
UniProt: Q9A9H3
Ligands: AKG, NA
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Perosamine synthetase	protein	368	42% helix, 17% strand	Q9A9H3
C	Perosamine synthetase	protein	365	42% helix, 16% strand	Q9A9H3
D	Perosamine synthetase	protein	364	42% helix, 16% strand	Q9A9H3

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · chains A, B
NA · Sodium ion · metal · chains A
ACT · Acetate ion · additive · 3 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	487	0.69	0.80	49	ACT
2	440	0.68	0.80	48	AKG
3	442	0.68	0.79	44	ACT
4	432	0.67	0.79	48	ACT
5	314	0.64	0.80	49	empty

Interfaces

4 interfaces between chains.

A–B · 2290 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2271 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 377 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 356 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (cofactor).

Compared structures

3BN1 · Crystal structure of GDP-perosamine synthase · the same entry in another collection · chain D against D, TM-score 1.00
Q9A9H3 · AlphaFold monomer V2.0 prediction for GDP-perosamine synthase (Q9A9H3) · a predicted model of the same protein · 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 Q9A9H3
Elsewhere: RCSB PDB 3BN1 · PDBe 3BN1 · UniProt Q9A9H3

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