MolNFT v1 · #145833 · protein

Crystal structure of medicago truncatula ATP-phosphoribosyltransferase in tense form

6CZM · ATP phosphoribosyltransferase catalytic subunit: “Crystal structure of medicago truncatula ATP-phosphoribosyltransferase in tense form”. X-ray diffraction, 2 ligands (AMP, HIS), 20 pockets (best druggability 0.84). MolNFT v1 #145833…

PDB: 6CZM
Type: protein
Length: 1,972 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP phosphoribosyltransferase catalytic subunit
UniProt: G7JFL4
Ligands: AMP, HIS
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 35% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP phosphoribosyltransferase catalytic subunit	protein	338	35% helix, 32% strand	G7JFL4
B	ATP phosphoribosyltransferase catalytic subunit	protein	307	36% helix, 32% strand	G7JFL4
C	ATP phosphoribosyltransferase catalytic subunit	protein	335	34% helix, 31% strand	G7JFL4
D	ATP phosphoribosyltransferase catalytic subunit	protein	335	35% helix, 31% strand	G7JFL4
E	ATP phosphoribosyltransferase catalytic subunit	protein	342	34% helix, 31% strand	G7JFL4
F	ATP phosphoribosyltransferase catalytic subunit	protein	315	34% helix, 30% strand	G7JFL4

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
HIS · Histidine · ligand · 6 copies · chains A, C, B, D, F, E

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

Pockets

20 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	1180	0.84	0.85	128	HIS
2	1094	0.84	0.85	108	HIS
3	321	0.56	0.76	37	empty
4	202	0.53	0.78	36	empty
5	247	0.52	0.76	24	empty

Interfaces

14 interfaces between chains.

D–E · 1488 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1470 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1460 Å² buried · 23 hydrogen bonds · protein-protein
D–F · 1257 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1231 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6CZM · Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in tense form · the same entry in another collection · chain C against C, 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 G7JFL4
Elsewhere: RCSB PDB 6CZM · PDBe 6CZM · UniProt G7JFL4

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