MolNFT v1 · #144934 · protein

The structure of mppp soaked with the product 2-ketoarginine

6C92 · Plp-dependent L-arginine hydroxylase mppp: “The structure of mppp soaked with the product 2-ketoarginine”. X-ray diffraction, 2 ligands (EGV, EQJ), 11 pockets (best druggability 0.83). MolNFT v1 #144934 on GenesisL1: 3D structure…

PDB: 6C92
Type: protein
Length: 1,444 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plp-dependent L-arginine hydroxylase mppp
UniProt: A0A0X1KHF5
Ligands: EGV, EQJ
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plp-dependent L-arginine hydroxylase mppp	protein	367	49% helix, 15% strand	A0A0X1KHF5
B	Plp-dependent L-arginine hydroxylase mppp	protein	369	47% helix, 15% strand	A0A0X1KHF5
C	Plp-dependent L-arginine hydroxylase mppp	protein	355	48% helix, 15% strand	A0A0X1KHF5
D	Plp-dependent L-arginine hydroxylase mppp	protein	353	48% helix, 15% strand	A0A0X1KHF5

Ligands and binding sites

EGV · (4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid · ligand · 2 copies · chains A, B, C, D
EQJ · (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)-L-arginine · ligand · chains A, B

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

Pockets

11 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	1140	0.83	0.84	154	empty
2	151	0.80	0.97	32	EQJ
3	754	0.75	0.80	70	empty
4	409	0.69	0.81	49	empty
5	466	0.66	0.79	58	EGV

Interfaces

5 interfaces between chains.

A–B · 2275 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1611 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 422 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 360 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 213 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 modified (cofactor).

Compared structures

6C92 · The structure of MppP soaked with the product 2-ketoarginine · 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 6C92 · PDBe 6C92 · UniProt A0A0X1KHF5

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