Research workbench

ATP-bound state of bip

Analyse ATP-bound state of bip in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E84
Type: protein
Length: 3,636 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 78 kda glucose-regulated protein
UniProt: P11021
Ligands: ATP, ZN, MG, SO4
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	78 kda glucose-regulated protein	protein	606	38% helix, 28% strand	P11021

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
ZN · Zinc ion · metal · 18 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	272	0.78	0.90	43	ATP, ZN
2	335	0.76	0.88	44	ATP, ZN
3	278	0.76	0.89	40	ATP, ZN
4	301	0.74	0.87	46	ATP, ZN
5	302	0.74	0.87	46	ATP, ZN

Interfaces

6 interfaces between chains.

D–F · 1270 Å² buried · 24 hydrogen bonds · protein-protein
A–E · 716 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 623 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 589 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 502 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5E84 · ATP-bound state of BiP · the same entry in another collection · chain E against E, TM-score 1.00
P11021 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (P11021) · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P11021
Elsewhere: RCSB PDB 5E84 · PDBe 5E84 · UniProt P11021

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