SMTL ID : 8jx8.1

rat megalin head

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

8 x UNK- UNK- LEU- UNK- UNK- UNK: unclear peptide(Non-covalent)

UNK-UNK-LEU-UNK-UNK-UNK.1: 6 residues within 4Å: Chain B: R.1556, W.1574, W.1600, C.1602, H.1645, R.1661 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.1574, B:W.1574, B:W.1600 Hydrogen bonds: B:R.1556, B:R.1556, B:R.1661, B:R.1661 UNK-UNK-LEU-UNK-UNK-UNK.2: 5 residues within 4Å: Chain B: H.1921, E.1923, H.1963, W.1965 Ligands: NI.48 No protein-ligand interaction detected (PLIP) UNK-UNK-LEU-UNK-UNK-UNK.3: 10 residues within 4Å: Chain B: L.2071, N.2097, F.2115, S.2117, N.2146, R.2149, R.2194, Y.2210, R.2296, R.2325 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.2071 Hydrogen bonds: B:N.2097, B:N.2146, B:R.2149, B:Y.2210 Salt bridges: B:R.2149, B:R.2194, B:R.2296, B:R.2325 UNK-UNK-LEU-UNK-UNK-UNK.4: 7 residues within 4Å: Chain B: I.2423, R.2511, W.2527, W.2553, N.2555, H.2595, F.2597 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.2423, B:W.2527, B:F.2597 Hydrogen bonds: B:R.2511, B:N.2555, B:N.2555 UNK-UNK-LEU-UNK-UNK-UNK.5: 6 residues within 4Å: Chain A: E.1513, R.1556, W.1574, W.1600, H.1645, R.1661 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.1574, A:W.1600 Hydrogen bonds: A:R.1556, A:R.1556, A:R.1661, A:R.1661 UNK-UNK-LEU-UNK-UNK-UNK.6: 4 residues within 4Å: Chain A: H.1921, E.1923, W.1965 Ligands: NI.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1921 UNK-UNK-LEU-UNK-UNK-UNK.7: 10 residues within 4Å: Chain A: L.2071, N.2097, F.2115, N.2146, R.2149, R.2194, Y.2210, Y.2282, R.2296, R.2325 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.2115 Hydrogen bonds: A:N.2097, A:N.2097, A:N.2146, A:R.2149, A:Y.2210 Salt bridges: A:R.2149, A:R.2194, A:R.2296, A:R.2325 UNK-UNK-LEU-UNK-UNK-UNK.8: 7 residues within 4Å: Chain A: R.2511, W.2527, W.2553, N.2555, H.2595, L.2611, Q.2637 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.2527 Hydrogen bonds: A:R.2511, A:R.2511, A:N.2555, A:N.2555

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

NAG-NAG.9: 4 residues within 4Å: Chain A: N.1436, N.1451, T.1453, Y.1460 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: K.1550, N.1551 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain A: H.1673, N.1676 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain A: N.1811 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain A: N.2396, N.2397, G.2420, T.2421 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain A: N.2548 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: N.1436, L.1438, N.1451, Y.1460 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain B: K.1550, N.1551 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain B: H.1673, N.1676 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 1 residues within 4Å: Chain B: N.1811 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain B: N.2396, N.2397, G.2420, T.2421 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 1 residues within 4Å: Chain B: N.2548 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.10: 2 residues within 4Å: Chain A: N.1497, T.1499 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain B: F.1495, N.1497, T.1499 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.13: 4 residues within 4Å: Chain A: N.1733, R.1743, Q.1746, F.1973 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 7 residues within 4Å: Chain A: N.2107, F.2109, K.2129, N.2134, I.2177, N.2178 Ligands: NAG.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.2129 NAG-NAG-BMA-MAN-MAN.22: 4 residues within 4Å: Chain B: N.1733, Q.1746, L.1762, D.1763 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.1975, B:Y.1975 NAG-NAG-BMA-MAN-MAN.24: 8 residues within 4Å: Chain B: N.2107, F.2109, R.2127, K.2129, N.2134, I.2177, N.2178 Ligands: NAG.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.2129

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

NAG.27: 1 residues within 4Å: Chain A: N.1384 No protein-ligand interaction detected (PLIP) NAG.28: 2 residues within 4Å: Chain A: N.2134 Ligands: NAG-NAG-BMA-MAN-MAN.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.2134 NAG.29: 1 residues within 4Å: Chain A: N.2225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.2225 NAG.30: 7 residues within 4Å: Chain A: N.2465, I.2466, G.2467, D.2485, N.2488, R.2501, H.2680 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.2465, A:R.2501 NAG.38: 1 residues within 4Å: Chain B: N.1384 No protein-ligand interaction detected (PLIP) NAG.39: 4 residues within 4Å: Chain B: S.2133, N.2134 Ligands: NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG.40: 1 residues within 4Å: Chain B: N.2225 No protein-ligand interaction detected (PLIP) NAG.41: 5 residues within 4Å: Chain B: L.2443, N.2465, I.2466, G.2467, N.2488 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.2465, B:G.2467

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G.31: 3 residues within 4Å: Chain A: F.2739, H.2740, T.2741 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.2719, A:T.2741 A2G.42: 2 residues within 4Å: Chain B: F.2739, T.2741 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.2741, B:T.2741

10 x CA: CALCIUM ION(Non-covalent)

CA.32: 6 residues within 4Å: Chain A: A.1331, D.1334, V.1336, D.1338, D.1344, E.1345 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.1331, A:D.1334, A:D.1338, A:D.1344, A:E.1345 CA.33: 7 residues within 4Å: Chain A: D.1391, I.1392, E.1394, N.1407, M.1408, G.1410, S.1411 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.1391, A:I.1392, A:E.1394, A:E.1394, A:M.1408 CA.34: 4 residues within 4Å: Chain A: D.2254, D.2257, P.2279 Chain B: N.2001 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.2254, A:D.2257, A:P.2279 CA.35: 7 residues within 4Å: Chain A: W.2718, C.2720, D.2721, D.2723, D.2725, D.2731, E.2732 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.2718, A:D.2721, A:D.2725, A:D.2731, A:E.2732 CA.36: 3 residues within 4Å: Chain A: A.1618, D.1621, H.1644 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.1618, A:D.1621, A:D.1621, A:H.1644 CA.43: 6 residues within 4Å: Chain B: D.1334, G.1335, V.1336, D.1338, D.1344, E.1345 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.1334, B:V.1336, B:D.1338, B:D.1344, B:E.1345 CA.44: 7 residues within 4Å: Chain B: D.1391, I.1392, E.1394, N.1407, M.1408, G.1410, S.1411 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.1391, B:E.1394, B:E.1394, B:M.1408, B:S.1411 CA.45: 4 residues within 4Å: Chain A: N.2001 Chain B: D.2254, D.2257, P.2279 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.2254, B:D.2257, B:P.2279 CA.46: 6 residues within 4Å: Chain B: W.2718, D.2721, D.2723, D.2725, D.2731, E.2732 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.2718, B:D.2723, B:D.2725, B:D.2731, B:E.2732 CA.47: 3 residues within 4Å: Chain B: A.1618, D.1621, H.1644 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:A.1618, B:D.1621, B:D.1621, B:H.1644

2 x NI: NICKEL (II) ION(Non-covalent)

NI.37: 4 residues within 4Å: Chain A: H.1921, E.1923, H.1963 Ligands: UNK-CYS-UNK.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.1921, A:E.1923, A:H.1963 NI.48: 5 residues within 4Å: Chain B: H.1921, E.1923, T.1939, H.1963 Ligands: UNK-CYS-UNK.2 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.1921, B:E.1923, B:H.1963

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto, S. et al., Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-06-19

Peptides

LDL receptor related protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LDL receptor related protein 2

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