MolNFT v1 · #141342 · protein

Crystal structure of prenyltransferase AMBP1 PH8 complexed with gspp and cis-indolyl vinyl isonitrile

5Z46: “Crystal structure of prenyltransferase AMBP1 PH8 complexed with gspp and cis-indolyl vinyl isonitrile”. X-ray diffraction, 3 ligands (GST, 8XL, MG), 5 pockets (best druggability 0.80). MolNFT v1 #141342 on GenesisL1: 3D structure…

PDB: 5Z46
Type: protein
Length: 581 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AMBP1
UniProt: V5TDZ4
Ligands: GST, 8XL, MG
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AMBP1	protein	290	38% helix, 31% strand	V5TDZ4
B	AMBP1	protein	291	38% helix, 30% strand	V5TDZ4

Ligands and binding sites

GST · Geranyl S-thiolodiphosphate · ligand · chains B
8XL · 3-[(Z)-2-isocyanoethenyl]-1H-indole · ligand · chains B
MG · Magnesium ion · metal · 4 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	868	0.80	0.82	88	GST, 8XL
2	412	0.70	0.81	38	empty
3	229	0.61	0.81	41	empty
4	54	0.30	0.76	15	empty
5	50	0.29	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 542 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5Z46 · Crystal structure of prenyltransferase AmbP1 pH8 complexed with GSPP and cis-indolyl… · 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 5Z46 · PDBe 5Z46 · UniProt V5TDZ4

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