SMTL ID : 6mpx.1

Twelve chloride ions induce formation and stabilize the NC1 hexamer of collagen IV assembled from transition state trimers

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: F.81, N.83, Y.653 Chain B: Y.202, A.203 Ligands: P6G.17 Ligand excluded by PLIP CL.2: 7 residues within 4Å: Chain A: A.538, S.539, R.540, N.541, D.542, G.642 Chain B: R.419 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: Y.429, F.528, N.530 Chain B: Y.425, A.426 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: Y.206, Y.305, N.307, Y.313 Chain B: Y.649, A.650 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: A.91, S.92, R.93, N.94, D.95, G.195 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: A.315, S.316, R.317, N.318, D.319 Chain B: R.643 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain A: Y.202, A.203 Chain B: F.81, N.83, Y.653 Ligands: P6G.38 Ligand excluded by PLIP CL.23: 7 residues within 4Å: Chain A: R.419 Chain B: A.538, S.539, R.540, N.541, D.542, G.642 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain A: Y.425, A.426 Chain B: Y.429, F.528, N.530 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain A: Y.649, A.650 Chain B: Y.206, Y.305, N.307, Y.313 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain B: A.91, S.92, R.93, N.94, D.95, G.195 Ligand excluded by PLIP CL.27: 6 residues within 4Å: Chain A: R.643 Chain B: A.315, S.316, R.317, N.318, D.319 Ligand excluded by PLIP

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 5 residues within 4Å: Chain A: E.438, Q.439, S.440, F.441, R.566 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: A.229, G.230, E.231, L.232, R.233 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: A.676, G.677, E.678, L.679, R.680 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: R.196, T.198, K.668 Chain B: K.668 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: S.596, G.597, W.598, R.692 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: Y.45, H.46 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: R.27, P.38 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: T.141, E.214, R.215, R.297 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain B: E.438, Q.439, S.440, F.441, R.566 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain B: A.229, G.230, E.231, L.232, R.233 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain B: A.676, G.677, E.678, L.679, R.680 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain A: K.668 Chain B: R.196, T.198, K.668 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain B: S.596, G.597, W.598, R.692 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain B: Y.45, H.46 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain B: R.27, P.38 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain B: T.141, E.214, R.215, R.297 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 5 residues within 4Å: Chain A: I.84, E.551, M.553, A.635, Y.648 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.85, A:N.85, A:M.553, A:M.553, A:Y.648 PEG.36: 5 residues within 4Å: Chain B: I.84, E.551, M.553, A.635, Y.648 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.85, B:N.85, B:M.553, B:M.553

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.16: 6 residues within 4Å: Chain A: P.103, E.104, A.188, Y.201, P.308 Ligands: P6G.38 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.186 PGE.37: 6 residues within 4Å: Chain B: P.103, E.104, A.188, Y.201, P.308 Ligands: P6G.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.186

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.17: 11 residues within 4Å: Chain A: N.83, N.85 Chain B: M.106, Y.201, Y.202, A.203, N.307, P.308, G.309 Ligands: CL.1, PGE.37 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.83 Water bridges: A:N.85, B:N.307 P6G.38: 11 residues within 4Å: Chain A: M.106, Y.201, Y.202, A.203, N.307, P.308, G.309 Chain B: N.83, N.85 Ligands: PGE.16, CL.22 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.83 Water bridges: B:N.85, A:N.307

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 7 residues within 4Å: Chain A: T.434, T.435, I.436, P.437, Q.442, H.458, F.537 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.435, A:Q.442, A:H.458 Water bridges: A:T.434, A:H.458 GOL.19: 7 residues within 4Å: Chain A: E.438, F.441, Q.442, G.443, S.444, G.562, E.563 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.438, A:G.443, A:S.444 GOL.20: 2 residues within 4Å: Chain A: Y.492, H.493 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.493, A:H.493 GOL.21: 3 residues within 4Å: Chain A: V.137, H.138, W.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.138 GOL.39: 7 residues within 4Å: Chain B: T.434, T.435, I.436, P.437, Q.442, H.458, F.537 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.435, B:Q.442, B:H.458, B:H.458 Water bridges: B:H.458 GOL.40: 7 residues within 4Å: Chain B: E.438, F.441, Q.442, G.443, S.444, G.562, E.563 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.438, B:E.438, B:G.443, B:S.444 GOL.41: 2 residues within 4Å: Chain B: Y.492, H.493 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.493 GOL.42: 3 residues within 4Å: Chain B: V.137, H.138, W.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedchenko, V. et al., A chloride ring is an ancient evolutionary innovation mediating the assembly of the collagen IV scaffold of basement membranes. J.Biol.Chem. (2019)

Release Date

2019-04-03

Peptides

fusion protein of non-collagenous domains of collagen type IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

fusion protein of non-collagenous domains of collagen type IV