MolNFT v1 · #79523 · protein

Crystal structure of a putative diacylglycerol kinase from bacillus anthracis str. sterne

3T5P · Bmru protein: “Crystal structure of a putative diacylglycerol kinase from bacillus anthracis str. sterne”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.75). MolNFT v1 #79523 on GenesisL1: 3D structure, binding…

PDB: 3T5P
Type: protein
Length: 3,448 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bmru protein
UniProt: Q81KC6
Ligands: MG
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 12 distinct chains · 26% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bmru protein	protein	287	23% helix, 34% strand	Q81KC6
B	Bmru protein	protein	299	26% helix, 33% strand	Q81KC6
C	Bmru protein	protein	292	28% helix, 33% strand	Q81KC6
D	Bmru protein	protein	293	26% helix, 33% strand	Q81KC6
E	Bmru protein	protein	295	26% helix, 33% strand	Q81KC6
F	Bmru protein	protein	273	25% helix, 34% strand	Q81KC6
G	Bmru protein	protein	291	27% helix, 34% strand	Q81KC6
H	Bmru protein	protein	272	25% helix, 35% strand	Q81KC6
I	Bmru protein	protein	277	26% helix, 35% strand	Q81KC6
J	Bmru protein	protein	278	24% helix, 35% strand	Q81KC6
K	Bmru protein	protein	289	26% helix, 34% strand	Q81KC6
L	Bmru protein	protein	302	24% helix, 32% strand	Q81KC6

Ligands and binding sites

MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	959	0.75	0.78	119	empty
2	768	0.71	0.77	91	empty
3	706	0.71	0.77	72	empty
4	781	0.71	0.77	93	empty
5	806	0.70	0.77	90	empty

Interfaces

13 interfaces between chains.

B–D · 923 Å² buried · 10 hydrogen bonds · protein-protein
E–K · 908 Å² buried · 8 hydrogen bonds · protein-protein
G–L · 903 Å² buried · 5 hydrogen bonds · protein-protein
A–J · 893 Å² buried · 4 hydrogen bonds · protein-protein
C–I · 889 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 25 modified (engineered).

Compared structures

3T5P · Crystal structure of a putative diacylglycerol kinase from Bacillus anthracis str. Sterne · 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 Q81KC6
Elsewhere: RCSB PDB 3T5P · PDBe 3T5P · UniProt Q81KC6

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