MolNFT v1 · #57339 · protein

Crystal structure of archaeal O-phosphoseryl-TRNA(SEC) kinase

3A4M · L-seryl-TRNA(SEC) kinase: “Crystal structure of archaeal O-phosphoseryl-TRNA(SEC) kinase”. X-ray diffraction, 3 ligands (ADP, MG, IOD), 6 pockets (best druggability 0.77). MolNFT v1 #57339 on GenesisL1: 3D structure, binding sites…

PDB: 3A4M
Type: protein
Length: 472 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-seryl-TRNA(SEC) kinase
EC: 2.7.1.-
UniProt: Q58933
Ligands: ADP, MG, IOD
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 58% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	L-seryl-TRNA(SEC) kinase (EC 2.7.1.-)	protein	236	58% helix, 11% strand	Q58933

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
IOD · Iodide ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 4 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	575	0.77	0.84	53	MG
2	715	0.76	0.81	67	EDO, ADP, MG
3	190	0.53	0.78	32	IOD
4	92	0.42	0.78	22	empty
5	56	0.31	0.76	14	EDO

Interfaces

1 interface between chains.

A–B · 1090 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3A4M · Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase · the same entry in another collection · chain A against A, TM-score 1.00
Q58933 · AlphaFold monomer V2.0 prediction for L-seryl-TRNA(SEC) kinase (Q58933) · a predicted model of the same protein · chain A against A, TM-score 0.73

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 Q58933
Elsewhere: RCSB PDB 3A4M · PDBe 3A4M · UniProt Q58933

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