MolNFT v1 · #141340 · protein

Crystal structure of prenyltransferase AMBP1 complexed with gspp

5Z44: “Crystal structure of prenyltransferase AMBP1 complexed with gspp”. X-ray diffraction, 2 ligands (GST, MG), 6 pockets (best druggability 0.80). MolNFT v1 #141340 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z44
Type: protein
Length: 580 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AMBP1
UniProt: V5TDZ4
Ligands: GST, MG
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	AMBP1	protein	290	34% helix, 31% strand	V5TDZ4

Ligands and binding sites

GST · Geranyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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	928	0.80	0.82	87	GST
2	535	0.75	0.82	52	GST
3	69	0.36	0.77	15	empty
4	72	0.34	0.75	14	empty
5	69	0.31	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 526 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5Z44 · Crystal structure of prenyltransferase AmbP1 complexed with GSPP · 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 V5TDZ4
Elsewhere: RCSB PDB 5Z44 · PDBe 5Z44 · UniProt V5TDZ4

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