MolNFT v1 · #114324 · protein

The structure of mppp E15A mutant soaked with the substrate L-arginine

5BK7 · Plp-dependent L-arginine hydroxylase mppp: “The structure of mppp E15A mutant soaked with the substrate L-arginine”. X-ray diffraction, 1 ligand (EQJ), 20 pockets (best druggability 0.83). MolNFT v1 #114324 on GenesisL1: 3D…

PDB: 5BK7
Type: protein
Length: 2,945 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plp-dependent L-arginine hydroxylase mppp
UniProt: A0A0X1KHF5
Ligands: EQJ
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Plp-dependent L-arginine hydroxylase mppp	protein	368	48% helix, 15% strand	A0A0X1KHF5
H	Plp-dependent L-arginine hydroxylase mppp	protein	369	49% helix, 15% strand	A0A0X1KHF5

Ligands and binding sites

EQJ · (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)-L-arginine · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	188	0.83	0.97	35	EQJ
2	188	0.83	0.97	34	EQJ
3	205	0.82	0.96	35	EQJ
4	182	0.82	0.97	35	EQJ
5	185	0.82	0.97	38	EQJ

Interfaces

9 interfaces between chains.

E–F · 2313 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2288 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 2282 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 2277 Å² buried · 30 hydrogen bonds · protein-protein
D–H · 798 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5BK7 · The structure of MppP E15A mutant soaked with the substrate L-arginine · 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 A0A0X1KHF5
Elsewhere: RCSB PDB 5BK7 · PDBe 5BK7 · UniProt A0A0X1KHF5

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