MolNFT v1 · #50280 · protein

Crystal structure of response regulator receiver protein from sinorhizobium medicae WSM419

2RDM: “Crystal structure of response regulator receiver protein from sinorhizobium medicae WSM419”. X-ray diffraction, 2 pockets (best druggability 0.54). MolNFT v1 #50280 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2RDM
Type: protein
Length: 369 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Response regulator receiver protein
UniProt: A6UIY7
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Response regulator receiver protein	protein	124	40% helix, 19% strand	A6UIY7
B	Response regulator receiver protein	protein	122	41% helix, 20% strand	A6UIY7
C	Response regulator receiver protein	protein	123	44% helix, 20% strand	A6UIY7

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	293	0.54	0.76	36	GOL
2	53	0.29	0.75	15	empty

Interfaces

3 interfaces between chains.

A–B · 570 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 527 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 38 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

2RDM · Crystal structure of response regulator receiver protein from Sinorhizobium medicae WSM419 · 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 A6UIY7
Elsewhere: RCSB PDB 2RDM · PDBe 2RDM · UniProt A6UIY7

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