MolNFT v1 · #54306 · protein

Ntca from synechococcus elongatus: active and inactive

2XKP · Global nitrogen regulator: “Ntca from synechococcus elongatus: active and inactive”. X-ray diffraction, 1 ligand (AKG), 20 pockets (best druggability 0.79). MolNFT v1 #54306 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2XKP
Type: protein
Length: 1,228 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Global nitrogen regulator
UniProt: P29283
Ligands: AKG
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Global nitrogen regulator	protein	207	41% helix, 29% strand	P29283
B, E	Global nitrogen regulator	protein	211	43% helix, 27% strand	P29283
C, F	Global nitrogen regulator	protein	196	39% helix, 29% strand	P29283

Ligands and binding sites

AKG · 2-oxoglutaric acid · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1095	0.79	0.81	90	empty
2	72	0.72	0.96	21	empty
3	66	0.70	0.96	18	empty
4	236	0.61	0.80	34	empty
5	228	0.60	0.80	34	empty

Interfaces

7 interfaces between chains.

D–E · 2174 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2174 Å² buried · 17 hydrogen bonds · protein-protein
C–F · 1311 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 501 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 389 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2XKP · NtcA from Synechococcus elongatus: active and inactive · the same entry in another collection · chain F against F, TM-score 1.00
P29283 · AlphaFold monomer V2.0 prediction for global nitrogen regulator (P29283) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P29283
Elsewhere: RCSB PDB 2XKP · PDBe 2XKP · UniProt P29283

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