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Crystal structure of the C-terminal domain of ypbh

Analyse Crystal structure of the C-terminal domain of ypbh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JTO
Type: protein
Length: 550 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adapter protein meca 2
UniProt: P50734
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 5 distinct chains · 42% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Adapter protein meca 2	protein	94	43% helix, 31% strand	P50734
B	Adapter protein meca 2	protein	90	43% helix, 24% strand	P50734
C	Adapter protein meca 2	protein	92	45% helix, 32% strand	P50734
E	Adapter protein meca 2	protein	89	40% helix, 24% strand	P50734
F	Adapter protein meca 2	protein	91	40% helix, 24% strand	P50734

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	103	0.58	0.85	18	empty
2	200	0.57	0.80	30	empty
3	229	0.55	0.78	41	empty
4	253	0.49	0.74	33	empty
5	113	0.34	0.72	24	empty

Interfaces

8 interfaces between chains.

C–D · 549 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 541 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 531 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 432 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 337 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3JTO · Crystal structure of the c-terminal domain of YpbH · the same entry in another collection · chain F against F, TM-score 1.00
P50734 · AlphaFold monomer V2.0 prediction for adapter protein meca 2 (P50734) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P50734
Elsewhere: RCSB PDB 3JTO · PDBe 3JTO · UniProt P50734

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