MolNFT v1 · #47912 · protein

Crystal structure of NE2512 protein of unknown function from nitrosomonas europaea

2PD1 · Hypothetical protein: “Crystal structure of NE2512 protein of unknown function from nitrosomonas europaea”. X-ray diffraction, 5 pockets (best druggability 0.84). MolNFT v1 #47912 on GenesisL1: 3D structure, binding sites and…

PDB: 2PD1
Type: protein
Length: 405 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein
UniProt: Q82S47
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein	protein	103	35% helix, 36% strand	Q82S47
B	Hypothetical protein	protein	100	36% helix, 37% strand	Q82S47
C, D	Hypothetical protein	protein	101	37% helix, 38% strand	Q82S47

Ligands and binding sites

ACT · Acetate ion · additive · 3 copies · chains A, B, C

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	244	0.84	0.95	41	ACT
2	322	0.61	0.79	37	empty
3	103	0.60	0.86	20	empty
4	96	0.57	0.85	18	ACT
5	76	0.33	0.75	16	empty

Interfaces

6 interfaces between chains.

A–C · 1504 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 1478 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 668 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 58 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 36 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

2PD1 · Crystal structure of NE2512 protein of unknown function from Nitrosomonas europaea · 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 Q82S47
Elsewhere: RCSB PDB 2PD1 · PDBe 2PD1 · UniProt Q82S47

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