SMTL ID : 8txn.1

Adaptive mechanism of collagen IV scaffold assembly in Drosophila: crystal structure of recombinant NC1 hexamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 7 residues within 4Å: Chain A: A.340, E.341, M.343, Q.425, Y.438, Q.558, N.559 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.559 Water bridges: A:M.343, A:A.424, A:N.560, A:N.560 PGE.6: 6 residues within 4Å: Chain A: D.63, A.172, Q.174, S.175, Q.303 Ligands: PG4.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.303, A:Q.303 PGE.8: 7 residues within 4Å: Chain A: H.610, S.611, E.615, V.616, P.617, D.618 Ligands: PEG.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.618 Water bridges: A:D.618, A:D.618 PGE.15: 5 residues within 4Å: Chain A: F.200, E.202, I.321, T.322 Chain B: N.85 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.85, A:F.200 PGE.17: 7 residues within 4Å: Chain B: N.411, D.537, G.539, S.540, P.541, S.649 Ligands: EDO.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.411 Water bridges: B:A.646

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

CL.2: 6 residues within 4Å: Chain A: L.551, A.565, S.566, R.567, N.568, D.569 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: L.77, A.91, S.92, R.93, N.94, D.95 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain B: L.551, A.565, S.566, R.567, N.568, D.569 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain B: L.77, A.91, S.92, R.93, N.94, D.95 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: D.531 Chain B: D.333 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.531, H2O.2, H2O.4, H2O.6, H2O.18, H2O.23 MG.13: 2 residues within 4Å: Chain A: D.333 Chain B: D.531 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.531, H2O.2, H2O.9, H2O.18, H2O.22, H2O.23

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 7 residues within 4Å: Chain A: N.411, L.498, D.537, G.539, S.540, S.649 Ligands: PGE.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.411 Water bridges: A:R.370 PG4.14: 7 residues within 4Å: Chain A: N.166, N.404, V.405 Chain B: N.166, R.295, N.404, V.405 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.166, B:N.166 Water bridges: A:A.296, A:A.296, A:Y.532, A:Y.532, A:Y.532, B:A.296, B:V.405, B:Y.532

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

PEG.7: 3 residues within 4Å: Chain A: N.211, S.233, H.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.233 Water bridges: A:N.211 PEG.9: 6 residues within 4Å: Chain A: W.45, P.72, V.609, H.610, L.647 Ligands: PGE.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.610 PEG.20: 3 residues within 4Å: Chain B: A.340, P.342 Ligands: EDO.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.340 Water bridges: B:M.343, B:M.343

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

EDO.10: 2 residues within 4Å: Chain A: P.581, Y.593 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.593 EDO.19: 4 residues within 4Å: Chain B: A.340, E.341, Y.438 Ligands: PEG.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.340 Water bridges: B:M.343 EDO.21: 6 residues within 4Å: Chain B: I.261, F.262, G.302, Q.303, S.414 Ligands: 1PE.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.261 EDO.22: 6 residues within 4Å: Chain B: V.606, Q.648, S.649, P.650 Ligands: PGE.17, 1PE.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.648

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.16: 9 residues within 4Å: Chain B: H.136, S.137, E.141, V.142, P.143, D.144, C.145, P.146, M.309 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.144, B:D.144 1PE.18: 14 residues within 4Å: Chain B: I.23, L.24, D.63, G.65, N.131, V.132, Q.174, S.175, P.176, Q.303, R.370, N.605 Ligands: EDO.21, EDO.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.370 Water bridges: B:L.24, B:Q.174

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.23: 5 residues within 4Å: Chain B: A.702, G.703, E.704, R.705, Q.706 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.701, B:G.703, B:E.704, B:R.705, B:Q.706, B:Q.706 Salt bridges: B:R.705

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Summers, J.A. et al., Collagen IV of basement membranes: IV. Adaptive mechanism of collagen IV scaffold assembly in Drosophila. J.Biol.Chem. (2023)

Release Date

2023-11-08

Peptides

Collagen alpha-1(IV) chain, Collagen IV - chain Viking, Collagen alpha-1(IV) chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Collagen alpha-1(IV) chain, Collagen IV - chain Viking, Collagen alpha-1(IV) chain