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N terminally deleted gapr crystal structure from C. crescentus

Analyse N terminally deleted gapr crystal structure from C. crescentus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OZZ
Type: protein
Length: 455 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0335 protein CC_3319
UniProt: Q9A385
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	UPF0335 protein CC_3319	protein	76	84% helix, 0% strand	Q9A385
B	UPF0335 protein CC_3319	protein	77	82% helix, 0% strand	Q9A385
D, F	UPF0335 protein CC_3319	protein	75	84% helix, 0% strand	Q9A385

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	398	0.64	0.78	48	empty
2	219	0.55	0.78	25	empty
3	208	0.54	0.78	24	empty
4	72	0.34	0.76	15	empty
5	52	0.25	0.73	13	empty

Interfaces

10 interfaces between chains.

D–F · 1368 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 1300 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 897 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 793 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 791 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6OZZ · N terminally deleted GapR crystal structure from C. crescentus · the same entry in another collection · chain F against F, TM-score 1.00
Q9A385 · AlphaFold monomer V2.0 prediction for UPF0335 protein CC_3319 (Q9A385) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 Q9A385
Elsewhere: RCSB PDB 6OZZ · PDBe 6OZZ · UniProt Q9A385

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