MolNFT v1 · #101527 · protein

Crystal structure of ptdh R301A

4NU5 · Phosphonate dehydrogenase: “Crystal structure of ptdh R301A”. X-ray diffraction, 1 ligand (NAD), 7 pockets (best druggability 0.74). MolNFT v1 #101527 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NU5
Type: protein
Length: 652 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphonate dehydrogenase
EC: 1.20.1.1
UniProt: O69054
Ligands: NAD
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphonate dehydrogenase (EC 1.20.1.1)	protein	328	35% helix, 16% strand	O69054
B	Phosphonate dehydrogenase (EC 1.20.1.1)	protein	324	36% helix, 16% strand	O69054

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	311	0.74	0.86	51	NAD
2	350	0.73	0.85	57	NAD
3	114	0.45	0.78	24	empty
4	134	0.42	0.75	24	empty
5	83	0.37	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 2640 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

4NU5 · Crystal Structure of PTDH R301A · the same entry in another collection · chain A against A, TM-score 1.00
O69054 · AlphaFold monomer V2.0 prediction for phosphonate dehydrogenase (O69054) · a predicted model of the same protein · chain B 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 O69054
Elsewhere: RCSB PDB 4NU5 · PDBe 4NU5 · UniProt O69054

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