MolNFT v1 · #27489 · protein

Crystal structure of dihydrodipicolinate synthase dapa-2 (BA3935) from bacillus anthracis.

1XL9: “Crystal structure of dihydrodipicolinate synthase dapa-2 (BA3935) from bacillus anthracis.”. X-ray diffraction, 9 pockets (best druggability 0.72). MolNFT v1 #27489 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1XL9
Type: protein
Length: 1,168 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrodipicolinate synthase
EC: 4.2.1.52
UniProt: Q81WN7
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Dihydrodipicolinate synthase (EC 4.2.1.52)	protein	292	49% helix, 13% strand	Q81WN7

Pockets

9 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	533	0.72	0.81	56	empty
2	573	0.71	0.80	63	empty
3	437	0.65	0.78	60	empty
4	228	0.55	0.78	33	empty
5	222	0.55	0.78	36	empty

Interfaces

4 interfaces between chains.

C–D · 1433 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1423 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 942 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 923 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1XL9 · Crystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935) from Bacillus Anthracis. · 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 Q81WN7
Elsewhere: RCSB PDB 1XL9 · PDBe 1XL9 · UniProt Q81WN7

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