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Crystal structure of the KCHIP1/KV4.3 T1 complex

Analyse Crystal structure of the KCHIP1/KV4.3 T1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2I2R
Type: protein
Length: 2,418 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Potassium voltage-gated channel subfamily D member 3; Kv channel-interacting protein 1
UniProt: Q62897, Q9NZI2
Ligands: CA, ZN, NA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 16 distinct chains · 50% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Potassium voltage-gated channel subfamily D member 3	protein	129	36% helix, 16% strand	Q62897
B	Potassium voltage-gated channel subfamily D member 3	protein	124	40% helix, 16% strand	Q62897
C	Potassium voltage-gated channel subfamily D member 3	protein	126	40% helix, 16% strand	Q62897
D	Potassium voltage-gated channel subfamily D member 3	protein	122	40% helix, 16% strand	Q62897
E	Kv channel-interacting protein 1	protein	179	58% helix, 6% strand	Q9NZI2
F	Kv channel-interacting protein 1	protein	180	60% helix, 6% strand	Q9NZI2
G	Kv channel-interacting protein 1	protein	174	58% helix, 6% strand	Q9NZI2
H	Kv channel-interacting protein 1	protein	174	58% helix, 6% strand	Q9NZI2
I	Potassium voltage-gated channel subfamily D member 3	protein	133	35% helix, 15% strand	Q62897
J	Potassium voltage-gated channel subfamily D member 3	protein	129	39% helix, 16% strand	Q62897
K	Potassium voltage-gated channel subfamily D member 3	protein	132	38% helix, 15% strand	Q62897
L	Potassium voltage-gated channel subfamily D member 3	protein	138	36% helix, 14% strand	Q62897
M	Kv channel-interacting protein 1	protein	170	61% helix, 6% strand	Q9NZI2
N	Kv channel-interacting protein 1	protein	168	60% helix, 6% strand	Q9NZI2
O	Kv channel-interacting protein 1	protein	168	59% helix, 6% strand	Q9NZI2
P	Kv channel-interacting protein 1	protein	172	60% helix, 6% strand	Q9NZI2

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains E, F, G, H, M, N, O, P
ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, I, J, K, L
NA · Sodium ion · metal · 4 copies · chains E, F, G, N, H, I

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1019	0.86	0.87	126	empty
2	1179	0.84	0.85	122	empty
3	1190	0.83	0.84	118	empty
4	949	0.82	0.83	106	NA
5	245	0.78	0.91	28	empty

Interfaces

46 interfaces between chains.

L–P · 1256 Å² buried · 8 hydrogen bonds · protein-protein
I–M · 1087 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 1063 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 1037 Å² buried · 10 hydrogen bonds · protein-protein
C–G · 992 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2I2R · Crystal structure of the KChIP1/Kv4.3 T1 complex · the same entry in another collection · chain K against K, 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 Q62897
Every structure of UniProt Q9NZI2
Elsewhere: RCSB PDB 2I2R · PDBe 2I2R · UniProt Q62897 · UniProt Q9NZI2

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