MolNFT v1 · #20989 · protein

Extracellular domain of mycobacterium tuberculosis pknd

1RWI · SERINE/THREONINE-protein kinase pknd: “Extracellular domain of mycobacterium tuberculosis pknd”. X-ray diffraction, 1 ligand (CD), 6 pockets (best druggability 0.76). MolNFT v1 #20989 on GenesisL1: 3D structure, binding sites and…

PDB: 1RWI
Type: protein
Length: 510 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase pknd
EC: 2.7.1.37
UniProt: O05871
Ligands: CD
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	SERINE/THREONINE-protein kinase pknd (EC 2.7.1.37)	protein	254	5% helix, 40% strand	O05871
A	SERINE/THREONINE-protein kinase pknd (EC 2.7.1.37)	protein	256	5% helix, 41% strand	O05871

Ligands and binding sites

CD · Cadmium ion · metal · 14 copies · chains B, A

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	495	0.76	0.84	52	empty
2	434	0.74	0.84	43	empty
3	216	0.61	0.82	37	CD
4	81	0.36	0.76	18	empty
5	68	0.34	0.76	17	empty

Interfaces

1 interface between chains.

B–A · 597 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1RWI · Extracellular domain of Mycobacterium tuberculosis PknD · the same entry in another collection · chain B against B, 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 O05871
Elsewhere: RCSB PDB 1RWI · PDBe 1RWI · UniProt O05871

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