MolNFT v1 · #153241 · protein

Crystal structure of blue fluorescent protein from metagenomic library in complex with NADPH

6J7U: “Crystal structure of blue fluorescent protein from metagenomic library in complex with NADPH”. X-ray diffraction, 1 ligand (NDP), 5 pockets (best druggability 0.85). MolNFT v1 #153241 on GenesisL1: 3D structure, binding sites and…

PDB: 6J7U
Type: protein
Length: 988 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Blue fluorescent protein
EC: 1.2.4.4
UniProt: D6NKF4
Ligands: NDP
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Blue fluorescent protein (EC 1.2.4.4)	protein	247	47% helix, 15% strand	D6NKF4

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1050	0.85	0.86	70	empty
2	1072	0.83	0.84	109	NDP
3	1016	0.83	0.84	106	NDP
4	154	0.51	0.79	20	empty
5	142	0.48	0.78	21	empty

Interfaces

6 interfaces between chains.

A–C · 1645 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 1640 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1599 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1593 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 243 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6J7U · Crystal structure of blue fluorescent protein from metagenomic library in complex with… · 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 D6NKF4
Elsewhere: RCSB PDB 6J7U · PDBe 6J7U · UniProt D6NKF4

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