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Crystal structure of putative nucleic acid-binding lipoprotein (YP_001337197.1) from klebsiella pneumoniae subsp. pneumoniae mgh 78578 at 2.46 a resolution

Analyse Crystal structure of putative nucleic acid-binding lipoprotein (YP_001337197.1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3F1Z
Type: protein
Length: 1,182 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative nucleic acid-binding lipoprotein
UniProt: A6TEE6
Pockets: 10 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 27% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, J	Putative nucleic acid-binding lipoprotein	protein	119	25% helix, 39% strand	A6TEE6
D	Putative nucleic acid-binding lipoprotein	protein	117	27% helix, 38% strand	A6TEE6
F	Putative nucleic acid-binding lipoprotein	protein	118	27% helix, 39% strand	A6TEE6
G, H	Putative nucleic acid-binding lipoprotein	protein	118	27% helix, 39% strand	A6TEE6
I	Putative nucleic acid-binding lipoprotein	protein	116	28% helix, 40% strand	A6TEE6

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains F, J

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

Pockets

10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	161	0.80	0.96	28	empty
2	173	0.77	0.93	29	empty
3	205	0.76	0.91	32	empty
4	233	0.74	0.89	39	empty
5	218	0.74	0.89	35	empty

Interfaces

15 interfaces between chains.

E–J · 624 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 620 Å² buried · 8 hydrogen bonds · protein-protein
B–G · 619 Å² buried · 8 hydrogen bonds · protein-protein
D–I · 619 Å² buried · 9 hydrogen bonds · protein-protein
C–H · 613 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

3F1Z · Crystal structure of putative nucleic acid-binding lipoprotein (YP_001337197.1) from… · 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 A6TEE6
Elsewhere: RCSB PDB 3F1Z · PDBe 3F1Z · UniProt A6TEE6

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