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Local refinement of AQP1 tetramer (C1; refinement mask included D1 of protein 4.2 and ankyrin-1 AR1-5) in class 2 of erythrocyte ankyrin-1 complex

Analyse Local refinement of AQP1 tetramer (C1; refinement mask included D1 of protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8CT2
Type: protein
Length: 988 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aquaporin-1
UniProt: P29972
Ligands: CLR
Pockets: 13 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, B, C, A	Aquaporin-1	protein	247	70% helix, 0% strand	P29972

Ligands and binding sites

CLR · Cholesterol · ligand · 4 copies · chains D, C, B, A

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	188	0.84	0.97	23	empty
2	700	0.74	0.80	69	empty
3	483	0.73	0.82	80	empty
4	379	0.64	0.79	50	empty
5	394	0.64	0.78	54	empty

Interfaces

6 interfaces between chains.

D–C · 1624 Å² buried · 13 hydrogen bonds · protein-protein
D–B · 1614 Å² buried · 16 hydrogen bonds · protein-protein
C–A · 1610 Å² buried · 16 hydrogen bonds · protein-protein
B–A · 1608 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 25 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

8CT2 · Local refinement of AQP1 tetramer (C1; refinement mask included D1 of protein 4.2 and… · the same entry in another collection · chain A against A, TM-score 1.00
P29972 · AlphaFold monomer V2.0 prediction for aquaporin-1 (P29972) · a predicted model of the same protein · chain B 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 P29972
Elsewhere: RCSB PDB 8CT2 · PDBe 8CT2 · UniProt P29972

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