MolNFT v1 · #96777 · protein

Crystal structure of F139G mutant of 3-deoxy-D-manno-octulosonate 8- phosphate synthase (KDO8PS) from neisseria meningitidis

4JTL · 2-dehydro-3-deoxyphosphooctonate aldolase: “Crystal structure of F139G mutant of 3-deoxy-D-manno-octulosonate 8- phosphate synthase (KDO8PS) from…”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.73). MolNFT v1…

PDB: 4JTL
Type: protein
Length: 1,012 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-dehydro-3-deoxyphosphooctonate aldolase
EC: 2.5.1.55
UniProt: Q9JZ55
Ligands: CL
Pockets: 12 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55)	protein	250	42% helix, 20% strand	Q9JZ55
B	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55)	protein	255	42% helix, 20% strand	Q9JZ55
C	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55)	protein	253	42% helix, 21% strand	Q9JZ55
D	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55)	protein	254	43% helix, 20% strand	Q9JZ55

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains B, D, C

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	506	0.73	0.82	55	empty
2	519	0.71	0.80	51	empty
3	460	0.69	0.80	41	empty
4	426	0.67	0.79	42	empty
5	319	0.61	0.78	40	empty

Interfaces

6 interfaces between chains.

B–D · 1462 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1461 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1340 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1335 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 234 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4JTL · Crystal structure of F139G mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase… · 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 Q9JZ55
Elsewhere: RCSB PDB 4JTL · PDBe 4JTL · UniProt Q9JZ55

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