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Structure of phqe REDUCTASE/DIELS-alderase from penicillium fellutanum in complex with NADP+ and premalbrancheamide

Analyse Structure of phqe REDUCTASE/DIELS-alderase from penicillium fellutanum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NKK
Type: protein
Length: 1,539 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short chain dehydrogenase
UniProt: L0E2Z4
Ligands: NAP, PM7
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Short chain dehydrogenase	protein	257	49% helix, 16% strand	L0E2Z4
C, E, F	Short chain dehydrogenase	protein	256	49% helix, 16% strand	L0E2Z4

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
PM7 · (5as,12as,13as)-12,12-dimethyl-2,3,11,12,12A,13-hexahydro-1H,5H,6H-5A,13A-(epiminomethano) indolizino[7,6-b]carbazol-14-one · 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

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	711	0.84	0.88	91	NAP, PM7
2	1113	0.84	0.85	81	empty
3	581	0.82	0.88	66	NAP, PM7
4	926	0.82	0.83	86	NAP, PM7
5	773	0.81	0.84	69	NAP, PM7

Interfaces

9 interfaces between chains.

A–B · 1525 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 1519 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1507 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1421 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 782 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6NKK · Structure of PhqE Reductase/Diels-Alderase from Penicillium fellutanum in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
L0E2Z4 · AlphaFold monomer V2.0 prediction for short-chain DEHYDROGENASE/REDUCTASE phqe (L0E2Z4) · a predicted model of the same protein · chain C 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 L0E2Z4
Elsewhere: RCSB PDB 6NKK · PDBe 6NKK · UniProt L0E2Z4

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