MolNFT v1 · #124022 · protein

Bifunctional LYSX/ARGX from thermococcus kodakarensis with lysw-gamma- aaa

5K2M · Rimk-related lysine biosynthesis protein: “Bifunctional LYSX/ARGX from thermococcus kodakarensis with lysw-gamma- aaa”. X-ray diffraction, 6 ligands (ADP, UN1, MG), 20 pockets (best druggability 0.83). MolNFT v1 #124022 on…

PDB: 5K2M
Type: protein
Length: 2,368 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rimk-related lysine biosynthesis protein; Probable lysine biosynthesis protein
UniProt: Q5JFW0, Q5JFV9
Ligands: ADP, UN1, MG, ZN, PO4, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 9 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, G, I, J	Rimk-related lysine biosynthesis protein	protein	273	39% helix, 28% strand	Q5JFW0
D	Rimk-related lysine biosynthesis protein	protein	270	39% helix, 26% strand	Q5JFW0
E	Probable lysine biosynthesis protein	protein	52	0% helix, 37% strand	Q5JFV9
F	Probable lysine biosynthesis protein	protein	53	0% helix, 36% strand	Q5JFV9
H	Rimk-related lysine biosynthesis protein	protein	272	40% helix, 28% strand	Q5JFW0
K	Probable lysine biosynthesis protein	protein	11	0% helix, 9% strand	Q5JFV9
L	Probable lysine biosynthesis protein	protein	30	0% helix, 23% strand	Q5JFV9
M	Probable lysine biosynthesis protein	protein	9	0% helix, 11% strand	Q5JFV9
N	Probable lysine biosynthesis protein	protein	33	0% helix, 33% strand	Q5JFV9

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, G, H, I, J
UN1 · 2-aminohexanedioic acid · ligand · 6 copies · chains A, E, B, F, I, G, K, H, L, J, N
MG · Magnesium ion · metal · 9 copies · chains A, B, G, H, J
ZN · Zinc ion · metal · 2 copies · chains E, F
PO4 · Phosphate ion · ion · 5 copies · chains A, E, B, F, G, K, I, J, N
SO4 · Sulfate ion · ion · 2 copies · chains C, H, L

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	591	0.83	0.88	85	ADP, SO4
2	950	0.80	0.81	90	ADP, PO4, UN1
3	803	0.79	0.82	83	ADP, PO4, MG, UN1
4	850	0.79	0.82	85	ADP
5	117	0.79	0.97	28	ADP, PO4, MG

Interfaces

35 interfaces between chains.

G–H · 1930 Å² buried · 19 hydrogen bonds · protein-protein
I–J · 1909 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1907 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1864 Å² buried · 21 hydrogen bonds · protein-protein
H–J · 1009 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

5K2M · Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA · 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 Q5JFW0
Every structure of UniProt Q5JFV9
Elsewhere: RCSB PDB 5K2M · PDBe 5K2M · UniProt Q5JFW0 · UniProt Q5JFV9

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