MolNFT v1 · #153815 · protein

Structure of paaz with NADPH

6JQM · Bifunctional protein paaz: “Structure of paaz with NADPH”. Electron microscopy, 1 ligand (NDP), 20 pockets (best druggability 0.85). MolNFT v1 #153815 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JQM
Type: protein
Length: 4,068 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional protein paaz
EC: 3.3.2.12
UniProt: P77455
Ligands: NDP
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Bifunctional protein paaz (EC 3.3.2.12)	protein	678	32% helix, 20% strand	P77455

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	859	0.85	0.88	76	empty
2	183	0.85	0.99	20	empty
3	732	0.84	0.87	96	empty
4	1165	0.84	0.85	108	empty
5	1160	0.84	0.85	103	empty

Interfaces

15 interfaces between chains.

A–B · 5046 Å² buried · 73 hydrogen bonds · protein-protein
E–F · 5034 Å² buried · 70 hydrogen bonds · protein-protein
C–D · 5032 Å² buried · 68 hydrogen bonds · protein-protein
A–C · 483 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 475 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6JQM · Structure of PaaZ with NADPH · the same entry in another collection · chain B against B, TM-score 1.00
P77455 · AlphaFold monomer V2.0 prediction for bifunctional protein paaz (P77455) · a predicted model of the same protein · chain A 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 P77455
Elsewhere: RCSB PDB 6JQM · PDBe 6JQM · UniProt P77455

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