SMTL ID : 6kkt.1

human KCC1 structure determined in KCl and lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: N.312, Y.356, E.392, K.393, H.394, S.398, A.399, D.400 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: L.359, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain B: N.312, Y.356, E.392, K.393, H.394, S.398, A.399, D.400 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: L.359, N.361 No protein-ligand interaction detected (PLIP)

4 x BGC- GLC: alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GLC.3: 6 residues within 4Å: Chain A: K.387, I.416, A.417, M.576 Ligands: BGC-GLC.8, DU0.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.387 BGC-GLC.4: 6 residues within 4Å: Chain A: W.635, Y.636, Y.637 Chain B: R.252, L.570 Ligands: DU0.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.252, B:L.570, B:R.252, B:R.252 BGC-GLC.7: 7 residues within 4Å: Chain A: R.252, L.570, I.571 Chain B: W.635, Y.636, Y.637 Ligands: DU0.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.252, A:L.570, A:R.252, A:R.252 BGC-GLC.8: 6 residues within 4Å: Chain B: K.387, I.416, A.417, M.576 Ligands: BGC-GLC.3, DU0.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.387

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 5 residues within 4Å: Chain A: F.205, G.433, I.434, M.435, Y.589 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: G.134, V.135, Y.216, P.429 Ligands: K.10 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: F.205, G.433, I.434, M.435, F.585, Y.589 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: G.134, V.135, Y.216, P.429 Ligands: K.14 Ligand excluded by PLIP

2 x K: POTASSIUM ION(Non-covalent)

K.10: 7 residues within 4Å: Chain A: N.131, I.132, Y.216, P.429, S.430, T.432 Ligands: CL.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.131, A:I.132, A:T.432 K.14: 7 residues within 4Å: Chain B: N.131, I.132, Y.216, P.429, S.430, T.432 Ligands: CL.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:N.131, B:I.132, B:T.432

2 x DU0: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol(Non-covalent)

DU0.12: 18 residues within 4Å: Chain A: L.203, Y.206, L.207, F.211, L.542, L.560, I.564, L.567, I.571, I.580, F.584, Y.637 Chain B: Y.636, Y.637, V.640, M.647 Ligands: BGC-GLC.3, BGC-GLC.7 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.203, A:Y.206, A:L.207, A:F.211, A:L.542, A:L.542, A:L.560, A:I.564, A:I.564, A:L.567, A:L.567, A:I.580, A:F.584, B:Y.636, B:V.640, B:V.640 DU0.16: 18 residues within 4Å: Chain A: Y.636, Y.637, V.640, M.647 Chain B: L.203, Y.206, L.207, F.211, L.542, L.560, I.564, L.567, I.571, I.580, F.584, Y.637 Ligands: BGC-GLC.4, BGC-GLC.8 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.203, B:Y.206, B:L.207, B:F.211, B:L.542, B:L.542, B:L.560, B:I.564, B:L.567, B:L.567, B:F.584, A:Y.636, A:V.640, A:V.640

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Cryo-EM structures of the human cation-chloride cotransporter KCC1. Science (2019)

Release Date

2019-10-23

Peptides

Solute carrier family 12 member 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Solute carrier family 12 member 4

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