MolNFT v1 · #154827 · protein

Crystal structure of sbnh in complex with citryl-diaminoethane

6KNK · Probable diaminopimelate decarboxylase protein: “Crystal structure of sbnh in complex with citryl-diaminoethane”. X-ray diffraction, 3 ligands (DN9, X3J, PO4), 13 pockets (best druggability 0.82). MolNFT v1 #154827 on GenesisL1: 3D…

PDB: 6KNK
Type: protein
Length: 1,148 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable diaminopimelate decarboxylase protein
UniProt: A0A0H3JPF2
Ligands: DN9, X3J, PO4
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable diaminopimelate decarboxylase protein	protein	383	35% helix, 27% strand	A0A0H3JPF2
B	Probable diaminopimelate decarboxylase protein	protein	383	33% helix, 28% strand	A0A0H3JPF2
C	Probable diaminopimelate decarboxylase protein	protein	382	34% helix, 27% strand	A0A0H3JPF2

Ligands and binding sites

DN9 · (2~{S})-2-[2-[2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]ethylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid · ligand · chains A, B
X3J · (2S)-2-{2-[(2-aminoethyl)amino]-2-oxoethyl}-2-hydroxybutanedioic acid · ligand · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	747	0.82	0.86	99	DN9, PO4, X3J
2	401	0.66	0.79	54	empty
3	445	0.63	0.77	41	empty
4	162	0.59	0.83	24	empty
5	128	0.57	0.84	25	empty

Interfaces

2 interfaces between chains.

A–B · 3042 Å² buried · 45 hydrogen bonds · protein-protein
B–C · 653 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6KNK · Crystal structure of SbnH in complex with citryl-diaminoethane · the same entry in another collection · chain C against C, 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 A0A0H3JPF2
Elsewhere: RCSB PDB 6KNK · PDBe 6KNK · UniProt A0A0H3JPF2

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