MolNFT v1 · #122478 · protein

Aminoglycoside phosphotransferase (2'')-ia (ctd of AAC(6')- IE/APH(2'')-ia) in complex with gmppnp, magnesium, and gentamicin C1

5IQC · Bifunctional AAC/APH: “Aminoglycoside phosphotransferase (2'')-ia (ctd of AAC(6')- IE/APH(2'')-ia) in complex with gmppnp…”. X-ray diffraction, 4 ligands (GNP, 51G, MG), 10 pockets (best druggability 0.77). MolNFT v1 #122478 on…

PDB: 5IQC
Type: protein
Length: 1,187 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional AAC/APH
EC: 2.3.1.-, 2.7.1.-
UniProt: P0A0C1
Ligands: GNP, 51G, MG, CL
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-)	protein	301	50% helix, 17% strand	P0A0C1
B	Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-)	protein	299	50% helix, 16% strand	P0A0C1
C	Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-)	protein	297	51% helix, 17% strand	P0A0C1
D	Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-)	protein	290	52% helix, 16% strand	P0A0C1

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
51G · gentamicin C1 · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
CL · Chloride ion · ion · 3 copies · chains A, C
GOL · Glycerol · additive · 2 copies · chains B, D

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

Pockets

10 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	788	0.77	0.81	77	empty
2	1192	0.76	0.78	81	GNP, 51G, MG
3	915	0.72	0.76	75	GNP, 51G, MG
4	829	0.70	0.76	70	GNP, 51G, MG
5	407	0.63	0.77	50	51G, MG

Interfaces

5 interfaces between chains.

A–B · 1260 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 786 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 234 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 163 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 26 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5IQC · Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex… · the same entry in another collection · chain D against D, TM-score 1.00
P0A0C1 · AlphaFold monomer V2.0 prediction for bifunctional AAC/APH (P0A0C1) · a predicted model of the same protein · chain D 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 P0A0C1
Elsewhere: RCSB PDB 5IQC · PDBe 5IQC · UniProt P0A0C1

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