SMTL ID : 6wku.1

Twelve Chloride Ions Drive Assembly of Human alpha345 Collagen IV NC1 domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 7 residues within 4Å: Chain A: A.91, S.92, R.93, N.94, D.95, G.195, R.196 Ligand excluded by PLIP CL.2: 7 residues within 4Å: Chain A: L.301, A.315, Q.316, R.317, N.318, D.319, R.418 Ligand excluded by PLIP CL.3: 7 residues within 4Å: Chain A: A.540, S.541, R.542, N.543, D.544, G.644 Chain B: R.645 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: S.203 Chain B: Y.206, Y.305, N.307 Ligands: PG4.56 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: F.425, A.426 Chain B: F.81, N.83, Y.655 Ligands: PGE.9 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: Y.651, A.652 Chain B: Y.429, F.530, N.532 Ligands: PGE.115 Ligand excluded by PLIP CL.94: 7 residues within 4Å: Chain B: A.91, S.92, R.93, N.94, D.95, G.195, R.196 Ligand excluded by PLIP CL.95: 7 residues within 4Å: Chain B: L.301, A.315, Q.316, R.317, N.318, D.319, R.418 Ligand excluded by PLIP CL.96: 7 residues within 4Å: Chain A: R.645 Chain B: A.540, S.541, R.542, N.543, D.544, G.644 Ligand excluded by PLIP CL.97: 5 residues within 4Å: Chain A: Y.206, Y.305, N.307 Chain B: S.203 Ligands: PG4.149 Ligand excluded by PLIP CL.98: 6 residues within 4Å: Chain A: F.81, N.83, Y.655 Chain B: F.425, A.426 Ligands: PGE.102 Ligand excluded by PLIP CL.99: 6 residues within 4Å: Chain A: Y.429, F.530, N.532 Chain B: Y.651, A.652 Ligands: PGE.22 Ligand excluded by PLIP

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

P6G.7: 13 residues within 4Å: Chain A: A.358, V.359, H.360, Q.362, L.397, L.473, V.493, Y.494, A.516, C.519, L.520, R.521 Ligands: PG4.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.360, A:R.521, A:R.521 P6G.100: 13 residues within 4Å: Chain B: A.358, V.359, H.360, Q.362, L.397, L.473, V.493, Y.494, A.516, C.519, L.520, R.521 Ligands: PG4.121 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.360, B:Y.494, B:R.521, B:R.521

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

PGE.8: 11 residues within 4Å: Chain A: H.60, D.287, G.394, Q.395, A.396, H.509, G.510, D.512, G.621, A.623 Ligands: PEG.13 Ligand excluded by PLIP PGE.9: 16 residues within 4Å: Chain A: L.330, P.331, M.332, H.423, F.424, F.425, A.426, I.533 Chain B: N.83, N.85, V.87, N.89, T.675 Ligands: CL.5, PEG.20, EDO.50 Ligand excluded by PLIP PGE.10: 5 residues within 4Å: Chain A: N.214, E.216, R.217, I.223 Ligands: PGE.11 Ligand excluded by PLIP PGE.11: 8 residues within 4Å: Chain A: S.212, I.223, S.225, I.235, Y.314 Ligands: PGE.10, PGE.18, PEG.23 Ligand excluded by PLIP PGE.15: 9 residues within 4Å: Chain A: I.133, Q.355, V.357, M.398, F.472, L.473 Ligands: PGE.36, PEG.46, EDO.78 Ligand excluded by PLIP PGE.18: 8 residues within 4Å: Chain A: S.225, V.227, E.231, I.235 Ligands: PGE.11, PG4.16, PEG.23, PGE.38 Ligand excluded by PLIP PGE.22: 10 residues within 4Å: Chain A: N.532, N.534, V.536 Chain B: V.84, N.85, M.555, M.559 Ligands: EDO.50, CL.99, PEG.127 Ligand excluded by PLIP PGE.24: 6 residues within 4Å: Chain A: R.267, L.268, W.269, T.270, P.296 Ligands: PGE.30 Ligand excluded by PLIP PGE.29: 4 residues within 4Å: Chain A: T.32, A.117, E.119, P.120 Ligand excluded by PLIP PGE.30: 5 residues within 4Å: Chain A: P.215, E.216, M.218 Ligands: PGE.24, PEG.61 Ligand excluded by PLIP PGE.33: 7 residues within 4Å: Chain A: D.63, A.134, I.135, A.176, S.177, P.178, L.290 Ligand excluded by PLIP PGE.36: 11 residues within 4Å: Chain A: G.22, F.23, V.24, T.66, V.582, V.583, I.584, A.625, S.626 Ligands: PGE.15, EDO.78 Ligand excluded by PLIP PGE.38: 6 residues within 4Å: Chain A: F.158, E.233, K.234, R.238 Ligands: PGE.18, PEG.32 Ligand excluded by PLIP PGE.41: 8 residues within 4Å: Chain A: I.34, S.46, G.47, F.48, Q.72, E.119, R.124 Ligands: PGE.42 Ligand excluded by PLIP PGE.42: 6 residues within 4Å: Chain A: Q.72, R.73, E.119, M.667, F.668 Ligands: PGE.41 Ligand excluded by PLIP PGE.48: 6 residues within 4Å: Chain A: P.470, G.471, G.489, E.578, A.579, P.580 Ligand excluded by PLIP PGE.54: 8 residues within 4Å: Chain A: A.328, L.330, F.407, R.408, A.409, A.410, S.454, N.535 Ligand excluded by PLIP PGE.55: 11 residues within 4Å: Chain A: R.21, F.23, F.247, A.354, Q.355, A.469, P.470, G.471, F.472, A.581, V.582 Ligand excluded by PLIP PGE.68: 9 residues within 4Å: Chain A: A.136, V.137, H.138, P.146, L.175, A.176, W.269, A.291, P.296 Ligand excluded by PLIP PGE.77: 3 residues within 4Å: Chain A: D.482 Ligands: PEG.76, PEG.88 Ligand excluded by PLIP PGE.101: 11 residues within 4Å: Chain B: H.60, D.287, G.394, Q.395, A.396, H.509, G.510, D.512, G.621, A.623 Ligands: PEG.106 Ligand excluded by PLIP PGE.102: 16 residues within 4Å: Chain A: N.83, N.85, V.87, N.89, T.675 Chain B: L.330, P.331, M.332, H.423, F.424, F.425, A.426, I.533 Ligands: CL.98, PEG.113, EDO.143 Ligand excluded by PLIP PGE.103: 5 residues within 4Å: Chain B: N.214, E.216, R.217, I.223 Ligands: PGE.104 Ligand excluded by PLIP PGE.104: 8 residues within 4Å: Chain B: S.212, I.223, S.225, I.235, Y.314 Ligands: PGE.103, PGE.111, PEG.116 Ligand excluded by PLIP PGE.108: 9 residues within 4Å: Chain B: I.133, Q.355, V.357, M.398, F.472, L.473 Ligands: PGE.129, PEG.139, EDO.171 Ligand excluded by PLIP PGE.111: 8 residues within 4Å: Chain B: S.225, V.227, E.231, I.235 Ligands: PGE.104, PG4.109, PEG.116, PGE.131 Ligand excluded by PLIP PGE.115: 10 residues within 4Å: Chain A: V.84, N.85, M.555, M.559 Chain B: N.532, N.534, V.536 Ligands: CL.6, PEG.34, EDO.143 Ligand excluded by PLIP PGE.117: 6 residues within 4Å: Chain B: R.267, L.268, W.269, T.270, P.296 Ligands: PGE.123 Ligand excluded by PLIP PGE.122: 4 residues within 4Å: Chain B: T.32, A.117, E.119, P.120 Ligand excluded by PLIP PGE.123: 5 residues within 4Å: Chain B: P.215, E.216, M.218 Ligands: PGE.117, PEG.154 Ligand excluded by PLIP PGE.126: 7 residues within 4Å: Chain B: D.63, A.134, I.135, A.176, S.177, P.178, L.290 Ligand excluded by PLIP PGE.129: 11 residues within 4Å: Chain B: G.22, F.23, V.24, T.66, V.582, V.583, I.584, A.625, S.626 Ligands: PGE.108, EDO.171 Ligand excluded by PLIP PGE.131: 6 residues within 4Å: Chain B: F.158, E.233, K.234, R.238 Ligands: PGE.111, PEG.125 Ligand excluded by PLIP PGE.134: 8 residues within 4Å: Chain B: I.34, S.46, G.47, F.48, Q.72, E.119, R.124 Ligands: PGE.135 Ligand excluded by PLIP PGE.135: 6 residues within 4Å: Chain B: Q.72, R.73, E.119, M.667, F.668 Ligands: PGE.134 Ligand excluded by PLIP PGE.141: 6 residues within 4Å: Chain B: P.470, G.471, G.489, E.578, A.579, P.580 Ligand excluded by PLIP PGE.147: 8 residues within 4Å: Chain B: A.328, L.330, F.407, R.408, A.409, A.410, S.454, N.535 Ligand excluded by PLIP PGE.148: 11 residues within 4Å: Chain B: R.21, F.23, F.247, A.354, Q.355, A.469, P.470, G.471, F.472, A.581, V.582 Ligand excluded by PLIP PGE.161: 9 residues within 4Å: Chain B: A.136, V.137, H.138, P.146, L.175, A.176, W.269, A.291, P.296 Ligand excluded by PLIP PGE.170: 3 residues within 4Å: Chain B: D.482 Ligands: PEG.169, PEG.181 Ligand excluded by PLIP

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

PG4.12: 5 residues within 4Å: Chain A: I.591, Q.592, I.605, Y.607, R.687 Ligand excluded by PLIP PG4.16: 7 residues within 4Å: Chain A: P.224, S.225, T.226, Q.316 Chain B: A.111, P.112 Ligands: PGE.18 Ligand excluded by PLIP PG4.27: 6 residues within 4Å: Chain A: S.361, D.363, S.365, A.438, R.521, R.522 Ligand excluded by PLIP PG4.28: 7 residues within 4Å: Chain A: C.369, P.370, Q.371, L.491, V.493, E.578 Ligands: P6G.7 Ligand excluded by PLIP PG4.51: 7 residues within 4Å: Chain A: P.131, G.150, W.151, I.152, G.244, T.245, E.351 Ligand excluded by PLIP PG4.52: 12 residues within 4Å: Chain A: R.21, F.23, A.132, I.133, G.244, T.245, G.246, F.247, G.264, E.351, A.352, P.353 Ligand excluded by PLIP PG4.53: 8 residues within 4Å: Chain A: Q.364, Y.380, D.406, Q.455, R.458, Q.459 Ligands: PEG.35, EDO.74 Ligand excluded by PLIP PG4.56: 14 residues within 4Å: Chain A: M.110, N.200, Y.201, Y.202, S.203, I.308, H.309 Chain B: N.307, H.309, H.313 Ligands: CL.4, 1PE.21, EDO.92, PEG.183 Ligand excluded by PLIP PG4.65: 7 residues within 4Å: Chain A: I.34, P.35, S.36, P.43, L.44, Y.45, S.46 Ligand excluded by PLIP PG4.72: 10 residues within 4Å: Chain A: L.251, H.252, S.253, T.255, P.259, A.327, E.405, D.406, R.408 Ligands: PEG.73 Ligand excluded by PLIP PG4.105: 5 residues within 4Å: Chain B: I.591, Q.592, I.605, Y.607, R.687 Ligand excluded by PLIP PG4.109: 7 residues within 4Å: Chain A: A.111, P.112 Chain B: P.224, S.225, T.226, Q.316 Ligands: PGE.111 Ligand excluded by PLIP PG4.120: 6 residues within 4Å: Chain B: S.361, D.363, S.365, A.438, R.521, R.522 Ligand excluded by PLIP PG4.121: 7 residues within 4Å: Chain B: C.369, P.370, Q.371, L.491, V.493, E.578 Ligands: P6G.100 Ligand excluded by PLIP PG4.144: 7 residues within 4Å: Chain B: P.131, G.150, W.151, I.152, G.244, T.245, E.351 Ligand excluded by PLIP PG4.145: 12 residues within 4Å: Chain B: R.21, F.23, A.132, I.133, G.244, T.245, G.246, F.247, G.264, E.351, A.352, P.353 Ligand excluded by PLIP PG4.146: 8 residues within 4Å: Chain B: Q.364, Y.380, D.406, Q.455, R.458, Q.459 Ligands: PEG.128, EDO.167 Ligand excluded by PLIP PG4.149: 14 residues within 4Å: Chain A: N.307, H.309, H.313 Chain B: M.110, N.200, Y.201, Y.202, S.203, I.308, H.309 Ligands: PEG.90, CL.97, 1PE.114, EDO.185 Ligand excluded by PLIP PG4.158: 7 residues within 4Å: Chain B: I.34, P.35, S.36, P.43, L.44, Y.45, S.46 Ligand excluded by PLIP PG4.165: 10 residues within 4Å: Chain B: L.251, H.252, S.253, T.255, P.259, A.327, E.405, D.406, R.408 Ligands: PEG.166 Ligand excluded by PLIP

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

PEG.13: 6 residues within 4Å: Chain A: D.287, A.396, M.398, S.399 Ligands: PGE.8, PEG.46 Ligand excluded by PLIP PEG.14: 7 residues within 4Å: Chain A: D.86, F.634, R.635, A.678, L.681, R.682 Ligands: PEG.40 Ligand excluded by PLIP PEG.20: 6 residues within 4Å: Chain A: M.332, M.333 Chain B: V.87, T.675, K.677 Ligands: PGE.9 Ligand excluded by PLIP PEG.23: 6 residues within 4Å: Chain A: S.212, L.213, N.214, K.234 Ligands: PGE.11, PGE.18 Ligand excluded by PLIP PEG.32: 4 residues within 4Å: Chain A: T.142, D.143, R.238 Ligands: PGE.38 Ligand excluded by PLIP PEG.34: 8 residues within 4Å: Chain A: V.84, P.552, E.553, P.554, A.637, Y.650 Ligands: PEG.40, PGE.115 Ligand excluded by PLIP PEG.35: 4 residues within 4Å: Chain A: Q.364, R.463 Ligands: PG4.53, EDO.74 Ligand excluded by PLIP PEG.37: 5 residues within 4Å: Chain A: R.27, A.33, I.34, P.35, S.36 Ligand excluded by PLIP PEG.39: 1 residues within 4Å: Chain A: T.32 Ligand excluded by PLIP PEG.40: 3 residues within 4Å: Chain A: D.86 Ligands: PEG.14, PEG.34 Ligand excluded by PLIP PEG.45: 4 residues within 4Å: Chain A: Q.485, C.486, P.487, Q.488 Ligand excluded by PLIP PEG.46: 8 residues within 4Å: Chain A: Q.355, A.356, V.357, M.398, P.400 Ligands: PEG.13, PGE.15, EDO.78 Ligand excluded by PLIP PEG.57: 6 residues within 4Å: Chain A: I.366, P.367, P.368, C.369, Q.465 Ligands: EDO.67 Ligand excluded by PLIP PEG.58: 4 residues within 4Å: Chain A: T.372, R.374 Ligands: PEG.59, EDO.60 Ligand excluded by PLIP PEG.59: 6 residues within 4Å: Chain A: T.372, W.373, R.374, V.468, P.470 Ligands: PEG.58 Ligand excluded by PLIP PEG.61: 5 residues within 4Å: Chain A: P.215, E.216, R.341 Ligands: PGE.30, EDO.44 Ligand excluded by PLIP PEG.63: 6 residues within 4Å: Chain A: H.60, G.61, D.63, T.171, G.172, A.174 Ligand excluded by PLIP PEG.73: 5 residues within 4Å: Chain A: T.260, C.261, P.262, E.405 Ligands: PG4.72 Ligand excluded by PLIP PEG.76: 4 residues within 4Å: Chain A: T.481, D.482, P.569 Ligands: PGE.77 Ligand excluded by PLIP PEG.81: 8 residues within 4Å: Chain A: Y.45, Q.72, H.587, S.588, P.594, H.595 Ligands: EDO.62, EDO.82 Ligand excluded by PLIP PEG.87: 4 residues within 4Å: Chain A: K.452, N.534, N.535 Ligands: EDO.50 Ligand excluded by PLIP PEG.88: 6 residues within 4Å: Chain A: T.481, D.482, A.483, R.573 Ligands: EDO.49, PGE.77 Ligand excluded by PLIP PEG.89: 2 residues within 4Å: Chain A: Q.310 Ligands: 1PE.21 Ligand excluded by PLIP PEG.90: 7 residues within 4Å: Chain A: K.228, A.229, H.309, Q.310 Chain B: M.108 Ligands: EDO.70, PG4.149 Ligand excluded by PLIP PEG.106: 6 residues within 4Å: Chain B: D.287, A.396, M.398, S.399 Ligands: PGE.101, PEG.139 Ligand excluded by PLIP PEG.107: 7 residues within 4Å: Chain B: D.86, F.634, R.635, A.678, L.681, R.682 Ligands: PEG.133 Ligand excluded by PLIP PEG.113: 6 residues within 4Å: Chain A: V.87, T.675, K.677 Chain B: M.332, M.333 Ligands: PGE.102 Ligand excluded by PLIP PEG.116: 6 residues within 4Å: Chain B: S.212, L.213, N.214, K.234 Ligands: PGE.104, PGE.111 Ligand excluded by PLIP PEG.125: 4 residues within 4Å: Chain B: T.142, D.143, R.238 Ligands: PGE.131 Ligand excluded by PLIP PEG.127: 8 residues within 4Å: Chain B: V.84, P.552, E.553, P.554, A.637, Y.650 Ligands: PGE.22, PEG.133 Ligand excluded by PLIP PEG.128: 4 residues within 4Å: Chain B: Q.364, R.463 Ligands: PG4.146, EDO.167 Ligand excluded by PLIP PEG.130: 5 residues within 4Å: Chain B: R.27, A.33, I.34, P.35, S.36 Ligand excluded by PLIP PEG.132: 1 residues within 4Å: Chain B: T.32 Ligand excluded by PLIP PEG.133: 3 residues within 4Å: Chain B: D.86 Ligands: PEG.107, PEG.127 Ligand excluded by PLIP PEG.138: 4 residues within 4Å: Chain B: Q.485, C.486, P.487, Q.488 Ligand excluded by PLIP PEG.139: 8 residues within 4Å: Chain B: Q.355, A.356, V.357, M.398, P.400 Ligands: PEG.106, PGE.108, EDO.171 Ligand excluded by PLIP PEG.150: 6 residues within 4Å: Chain B: I.366, P.367, P.368, C.369, Q.465 Ligands: EDO.160 Ligand excluded by PLIP PEG.151: 4 residues within 4Å: Chain B: T.372, R.374 Ligands: PEG.152, EDO.153 Ligand excluded by PLIP PEG.152: 6 residues within 4Å: Chain B: T.372, W.373, R.374, V.468, P.470 Ligands: PEG.151 Ligand excluded by PLIP PEG.154: 5 residues within 4Å: Chain B: P.215, E.216, R.341 Ligands: PGE.123, EDO.137 Ligand excluded by PLIP PEG.156: 6 residues within 4Å: Chain B: H.60, G.61, D.63, T.171, G.172, A.174 Ligand excluded by PLIP PEG.166: 5 residues within 4Å: Chain B: T.260, C.261, P.262, E.405 Ligands: PG4.165 Ligand excluded by PLIP PEG.169: 4 residues within 4Å: Chain B: T.481, D.482, P.569 Ligands: PGE.170 Ligand excluded by PLIP PEG.174: 8 residues within 4Å: Chain B: Y.45, Q.72, H.587, S.588, P.594, H.595 Ligands: EDO.155, EDO.175 Ligand excluded by PLIP PEG.180: 4 residues within 4Å: Chain B: K.452, N.534, N.535 Ligands: EDO.143 Ligand excluded by PLIP PEG.181: 6 residues within 4Å: Chain B: T.481, D.482, A.483, R.573 Ligands: EDO.142, PGE.170 Ligand excluded by PLIP PEG.182: 2 residues within 4Å: Chain B: Q.310 Ligands: 1PE.114 Ligand excluded by PLIP PEG.183: 7 residues within 4Å: Chain A: M.108 Chain B: K.228, A.229, H.309, Q.310 Ligands: PG4.56, EDO.163 Ligand excluded by PLIP

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

EDO.17: 2 residues within 4Å: Chain A: Q.364, Q.459 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: S.602, L.603 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain A: L.330, Y.343 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: A.328, P.329, P.342, Y.343 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: A.104, L.105, P.120, Y.121 Ligands: EDO.66, EDO.83 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain A: S.375, L.376, W.377 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain A: E.258, R.346 Ligands: PEG.61 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain A: Q.492, Y.494, E.495 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain A: F.497, Q.568, R.573 Ligands: PEG.88 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain A: N.534 Ligands: PGE.9, PGE.22, PEG.87 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain A: L.263, G.264, R.374 Ligands: PEG.58 Ligand excluded by PLIP EDO.62: 7 residues within 4Å: Chain A: Y.45, L.67, C.70, L.71, V.586, H.587 Ligands: PEG.81 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain A: S.444, A.445, P.446, A.447, P.448 Ligands: EDO.79 Ligand excluded by PLIP EDO.66: 3 residues within 4Å: Chain A: P.103, A.104 Ligands: EDO.31 Ligand excluded by PLIP EDO.67: 4 residues within 4Å: Chain A: W.373, R.374, S.375 Ligands: PEG.57 Ligand excluded by PLIP EDO.69: 3 residues within 4Å: Chain A: L.440, S.444, A.445 Ligand excluded by PLIP EDO.70: 4 residues within 4Å: Chain A: K.228 Chain B: M.108, N.109 Ligands: PEG.90 Ligand excluded by PLIP EDO.74: 4 residues within 4Å: Chain A: I.378, R.463 Ligands: PEG.35, PG4.53 Ligand excluded by PLIP EDO.75: 3 residues within 4Å: Chain A: K.563, R.645, T.647 Ligand excluded by PLIP EDO.78: 7 residues within 4Å: Chain A: L.473, I.474, G.514, T.515 Ligands: PGE.15, PGE.36, PEG.46 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain A: A.447, P.448 Ligands: EDO.64, EDO.84 Ligand excluded by PLIP EDO.80: 5 residues within 4Å: Chain A: Q.57, R.58, E.169, A.617 Chain B: D.390 Ligand excluded by PLIP EDO.82: 5 residues within 4Å: Chain A: S.588, T.590, Q.592, I.593 Ligands: PEG.81 Ligand excluded by PLIP EDO.83: 5 residues within 4Å: Chain A: L.105, M.106, P.107, Y.121 Ligands: EDO.31 Ligand excluded by PLIP EDO.84: 4 residues within 4Å: Chain A: A.447, P.448, D.449 Ligands: EDO.79 Ligand excluded by PLIP EDO.85: 2 residues within 4Å: Chain A: S.673 Chain B: Q.419 Ligand excluded by PLIP EDO.86: 1 residues within 4Å: Chain A: E.184 Ligand excluded by PLIP EDO.91: 2 residues within 4Å: Chain A: P.554, M.555 Ligand excluded by PLIP EDO.92: 5 residues within 4Å: Chain A: M.106, P.107, M.108 Ligands: 1PE.21, PG4.56 Ligand excluded by PLIP EDO.93: 4 residues within 4Å: Chain A: S.153, L.154, W.155, K.156 Ligand excluded by PLIP EDO.110: 2 residues within 4Å: Chain B: Q.364, Q.459 Ligand excluded by PLIP EDO.112: 2 residues within 4Å: Chain B: S.602, L.603 Ligand excluded by PLIP EDO.118: 2 residues within 4Å: Chain B: L.330, Y.343 Ligand excluded by PLIP EDO.119: 4 residues within 4Å: Chain B: A.328, P.329, P.342, Y.343 Ligand excluded by PLIP EDO.124: 6 residues within 4Å: Chain B: A.104, L.105, P.120, Y.121 Ligands: EDO.159, EDO.176 Ligand excluded by PLIP EDO.136: 3 residues within 4Å: Chain B: S.375, L.376, W.377 Ligand excluded by PLIP EDO.137: 3 residues within 4Å: Chain B: E.258, R.346 Ligands: PEG.154 Ligand excluded by PLIP EDO.140: 3 residues within 4Å: Chain B: Q.492, Y.494, E.495 Ligand excluded by PLIP EDO.142: 4 residues within 4Å: Chain B: F.497, Q.568, R.573 Ligands: PEG.181 Ligand excluded by PLIP EDO.143: 4 residues within 4Å: Chain B: N.534 Ligands: PGE.102, PGE.115, PEG.180 Ligand excluded by PLIP EDO.153: 4 residues within 4Å: Chain B: L.263, G.264, R.374 Ligands: PEG.151 Ligand excluded by PLIP EDO.155: 7 residues within 4Å: Chain B: Y.45, L.67, C.70, L.71, V.586, H.587 Ligands: PEG.174 Ligand excluded by PLIP EDO.157: 6 residues within 4Å: Chain B: S.444, A.445, P.446, A.447, P.448 Ligands: EDO.172 Ligand excluded by PLIP EDO.159: 3 residues within 4Å: Chain B: P.103, A.104 Ligands: EDO.124 Ligand excluded by PLIP EDO.160: 4 residues within 4Å: Chain B: W.373, R.374, S.375 Ligands: PEG.150 Ligand excluded by PLIP EDO.162: 3 residues within 4Å: Chain B: L.440, S.444, A.445 Ligand excluded by PLIP EDO.163: 4 residues within 4Å: Chain A: M.108, N.109 Chain B: K.228 Ligands: PEG.183 Ligand excluded by PLIP EDO.167: 4 residues within 4Å: Chain B: I.378, R.463 Ligands: PEG.128, PG4.146 Ligand excluded by PLIP EDO.168: 3 residues within 4Å: Chain B: K.563, R.645, T.647 Ligand excluded by PLIP EDO.171: 7 residues within 4Å: Chain B: L.473, I.474, G.514, T.515 Ligands: PGE.108, PGE.129, PEG.139 Ligand excluded by PLIP EDO.172: 4 residues within 4Å: Chain B: A.447, P.448 Ligands: EDO.157, EDO.177 Ligand excluded by PLIP EDO.173: 5 residues within 4Å: Chain A: D.390 Chain B: Q.57, R.58, E.169, A.617 Ligand excluded by PLIP EDO.175: 5 residues within 4Å: Chain B: S.588, T.590, Q.592, I.593 Ligands: PEG.174 Ligand excluded by PLIP EDO.176: 5 residues within 4Å: Chain B: L.105, M.106, P.107, Y.121 Ligands: EDO.124 Ligand excluded by PLIP EDO.177: 4 residues within 4Å: Chain B: A.447, P.448, D.449 Ligands: EDO.172 Ligand excluded by PLIP EDO.178: 2 residues within 4Å: Chain A: Q.419 Chain B: S.673 Ligand excluded by PLIP EDO.179: 1 residues within 4Å: Chain B: E.184 Ligand excluded by PLIP EDO.184: 2 residues within 4Å: Chain B: P.554, M.555 Ligand excluded by PLIP EDO.185: 5 residues within 4Å: Chain B: M.106, P.107, M.108 Ligands: 1PE.114, PG4.149 Ligand excluded by PLIP EDO.186: 4 residues within 4Å: Chain B: S.153, L.154, W.155, K.156 Ligand excluded by PLIP

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

1PE.21: 14 residues within 4Å: Chain A: P.103, A.104, L.105, F.185, R.186, A.187, S.188, Y.201, I.308, H.309, Q.310 Ligands: PG4.56, PEG.89, EDO.92 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.187, A:Q.310 Water bridges: A:S.188, A:S.188, A:S.188, A:Q.310 1PE.114: 14 residues within 4Å: Chain B: P.103, A.104, L.105, F.185, R.186, A.187, S.188, Y.201, I.308, H.309, Q.310 Ligands: PG4.149, PEG.182, EDO.185 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.187, B:H.309, B:Q.310 Water bridges: B:S.188, B:S.188, B:S.188, B:Q.310

2 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.71: 11 residues within 4Å: Chain A: Q.488, G.489, I.593, P.594, H.595, C.596, W.600, D.601, S.602, Q.689, M.692 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.595, A:C.596, A:S.602, A:Q.689 PE8.164: 11 residues within 4Å: Chain B: Q.488, G.489, I.593, P.594, H.595, C.596, W.600, D.601, S.602, Q.689, M.692 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.596, B:D.601, B:S.602, B:Q.689

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boudko, S.P. et al., Collagen IV alpha 345 dysfunction in glomerular basement membrane diseases. II. Crystal structure of the alpha 345 hexamer. J.Biol.Chem. (2021)

Release Date

2021-04-07

Peptides

Collagen alpha-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Collagen alpha-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chain