MolNFT v1 · #128788 · protein

Crystal structure of bifunctional dehydratase-cyclase domain in ambruticin biosynthesis

5O16 · Ambc: “Crystal structure of bifunctional dehydratase-cyclase domain in ambruticin biosynthesis”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.70). MolNFT v1 #128788 on GenesisL1: 3D structure, binding sites and…

PDB: 5O16
Type: protein
Length: 551 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ambc
UniProt: A1YBQ4
Ligands: SO4
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ambc	protein	279	18% helix, 42% strand	A1YBQ4
B	Ambc	protein	272	19% helix, 39% strand	A1YBQ4

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.70	0.82	39	SO4
2	214	0.68	0.85	36	empty
3	78	0.42	0.80	16	empty
4	108	0.40	0.76	21	empty
5	50	0.39	0.82	15	empty

Interfaces

1 interface between chains.

A–B · 1035 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5O16 · Crystal structure of bifunctional dehydratase-cyclase domain in ambruticin biosynthesis · 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 A1YBQ4
Elsewhere: RCSB PDB 5O16 · PDBe 5O16 · UniProt A1YBQ4

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