SMTL ID : 9foi.1

Structure of human KCTD1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-pentamer

Ligands

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 5 residues within 4Å: Chain A: G.223 Chain B: G.223 Chain C: G.223 Chain D: G.223 Ligands: NA.9 Ligand excluded by PLIP IOD.7: 6 residues within 4Å: Chain A: G.225 Chain B: G.225 Chain C: G.224, G.225 Chain D: G.225 Chain E: G.225 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: S.221 Chain B: S.221 Chain C: S.221 Chain D: S.221 Chain E: S.221 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.221 NA.3: 4 residues within 4Å: Chain A: P.32, V.33, H.34, Y.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.32, A:H.34, A:H.34 NA.9: 6 residues within 4Å: Chain A: G.223 Chain B: G.223 Chain C: G.223 Chain D: G.223 Chain E: G.223 Ligands: IOD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.223

5 x SIN: SUCCINIC ACID(Non-covalent)

SIN.4: 9 residues within 4Å: Chain A: V.37, G.38, H.40, D.81, G.82, Q.83 Chain E: H.40, Y.42, R.86 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:H.40, A:Q.83 Hydrogen bonds: A:G.38, A:G.82, A:Q.83, A:Q.83 Salt bridges: A:H.40, E:H.40 SIN.5: 11 residues within 4Å: Chain A: H.40, M.41, Y.42, R.86 Chain B: V.37, G.38, G.39, H.40, D.81, G.82, Q.83 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.42, B:H.40 Salt bridges: A:H.40, B:H.40 Hydrogen bonds: B:D.81, B:G.82, B:Q.83, B:Q.83 SIN.8: 11 residues within 4Å: Chain B: Y.42, R.86, L.89, R.93 Chain C: V.37, G.38, H.40, R.80, D.81, G.82, Q.83 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:Q.83, B:Y.42, B:R.86 Hydrogen bonds: C:D.81, C:G.82 Salt bridges: B:H.40, B:R.86, B:R.93 SIN.10: 10 residues within 4Å: Chain C: H.40, Y.42, R.86 Chain D: V.37, G.38, G.39, H.40, D.81, G.82, Q.83 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain D Salt bridges: C:H.40, D:H.40 Hydrophobic interactions: D:H.40, D:Q.83 Hydrogen bonds: D:V.37, D:D.81, D:G.82, D:Q.83, D:Q.83 SIN.11: 8 residues within 4Å: Chain D: H.40, Y.42, R.86 Chain E: G.38, H.40, D.81, G.82, Q.83 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:H.40, E:Q.83 Hydrogen bonds: E:H.40, E:G.82, E:Q.83 Water bridges: E:D.81, E:D.81 Salt bridges: E:H.40, D:H.40, D:R.86, D:R.86

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 1 residues within 4Å: Chain B: L.26 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain A: K.73 Chain E: M.41, H.75 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinkas, D.M. et al., A BTB extension and ion-binding domain contribute to the pentameric structure and TFAP2A binding of KCTD1. Structure (2024)

Release Date

2025-06-25

Peptides

BTB/POZ domain-containing protein KCTD1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

BTB/POZ domain-containing protein KCTD1