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Crystal structure of prenyltransferase AMBP1 apo structure

Analyse Crystal structure of prenyltransferase AMBP1 apo structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z43
Type: protein
Length: 581 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AMBP1
UniProt: V5TDZ4
Ligands: MG
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AMBP1	protein	292	36% helix, 28% strand	V5TDZ4
B	AMBP1	protein	289	37% helix, 29% strand	V5TDZ4

Ligands and binding sites

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

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	480	0.78	0.85	55	empty
2	409	0.69	0.81	35	empty
3	220	0.68	0.85	31	empty
4	364	0.67	0.81	37	empty
5	74	0.38	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 412 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5Z43 · Crystal structure of prenyltransferase AmbP1 apo structure · 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 5Z43 · PDBe 5Z43 · UniProt V5TDZ4

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