MolNFT v1 · #29828 · protein

Structural analysis of escherichia COLI thif

1ZKM · Adenylyltransferase thif: “Structural analysis of escherichia COLI thif”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.84). MolNFT v1 #29828 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZKM
Type: protein
Length: 954 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylyltransferase thif
EC: 2.7.7.-
UniProt: P30138
Ligands: ZN
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylyltransferase thif (EC 2.7.7.-)	protein	244	37% helix, 20% strand	P30138
B	Adenylyltransferase thif (EC 2.7.7.-)	protein	231	39% helix, 21% strand	P30138
C	Adenylyltransferase thif (EC 2.7.7.-)	protein	243	38% helix, 19% strand	P30138
D	Adenylyltransferase thif (EC 2.7.7.-)	protein	236	39% helix, 19% strand	P30138

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

9 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	865	0.84	0.86	78	empty
2	339	0.59	0.77	39	empty
3	352	0.58	0.76	41	empty
4	220	0.53	0.77	33	empty
5	189	0.52	0.78	30	empty

Interfaces

5 interfaces between chains.

C–D · 2820 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2707 Å² buried · 29 hydrogen bonds · protein-protein
A–D · 711 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 629 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 127 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1ZKM · Structural Analysis of Escherichia Coli ThiF · the same entry in another collection · chain D against D, TM-score 1.00
P30138 · AlphaFold monomer V2.0 prediction for sulfur carrier protein this adenylyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P30138
Elsewhere: RCSB PDB 1ZKM · PDBe 1ZKM · UniProt P30138

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