SMTL ID : 8jx9.1

rat megalin bodyA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

1 x UNK- UNK- ASN- UNK- UNK: ligand(Non-covalent)

UNK-UNK-ASN-UNK-UNK.1: 10 residues within 4Å: Chain B: R.3326, W.3342, W.3368, N.3370, A.3386, H.3411, W.3427, F.3454, R.3738, W.3739 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.3342, B:F.3454 Hydrogen bonds: B:R.3326, B:R.3326, B:N.3370, B:R.3738, B:R.3738

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.2: 2 residues within 4Å: Chain B: N.3127, L.3140 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain B: E.3200, Y.3202, N.3213, I.3224, L.3258 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.3200

3 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.4: 5 residues within 4Å: Chain B: E.3240, K.3241, F.3257, N.3259, T.3261 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.3240 NAG-NAG-BMA-MAN-MAN.7: 6 residues within 4Å: Chain B: D.3564, G.3565, N.3566, A.3581, A.3847, Q.3858 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 5 residues within 4Å: Chain B: P.3551, F.3838, N.3840, P.3845, A.3846 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.3846

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

NAG-NAG.5: 1 residues within 4Å: Chain B: N.3317 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: R.3350, N.3357, S.3359, A.3486 No protein-ligand interaction detected (PLIP)

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

NAG.9: 1 residues within 4Å: Chain B: N.3448 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.3448 NAG.10: 2 residues within 4Å: Chain B: N.3682, H.3683 No protein-ligand interaction detected (PLIP)

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

A2G.11: 1 residues within 4Å: Chain B: T.1225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.1225, B:T.1225 A2G.12: 2 residues within 4Å: Chain B: T.1271, C.1272 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.1272 A2G.13: 3 residues within 4Å: Chain B: T.3636, R.3638, P.3639 No protein-ligand interaction detected (PLIP) A2G.14: 1 residues within 4Å: Chain B: T.3799 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.3799, B:T.3799 A2G.15: 4 residues within 4Å: Chain B: T.3836, R.3837, F.3838, P.3839 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.3836

20 x CA: CALCIUM ION(Non-covalent)

CA.16: 6 residues within 4Å: Chain B: W.1249, D.1252, H.1254, D.1256, D.1262, E.1263 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.1249, B:D.1252, B:H.1254, B:D.1256, B:D.1262 CA.17: 7 residues within 4Å: Chain B: W.2925, C.2927, D.2928, D.2930, D.2932, D.2938, E.2939 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.2925, B:D.2928, B:D.2932, B:D.2938, B:E.2939 CA.18: 6 residues within 4Å: Chain B: W.2972, D.2975, D.2977, D.2979, D.2985, E.2986 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.2972, B:D.2975, B:D.2977, B:D.2979, B:D.2985 CA.19: 7 residues within 4Å: Chain B: F.3012, R.3013, D.3015, R.3017, D.3019, D.3025, E.3026 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3015, B:R.3017, B:D.3019, B:D.3025, B:E.3026 CA.20: 7 residues within 4Å: Chain B: F.3051, C.3053, D.3054, D.3056, D.3058, D.3064, E.3065 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.3051, B:D.3054, B:D.3058, B:D.3064, B:E.3065 CA.21: 6 residues within 4Å: Chain B: R.3094, N.3097, V.3099, D.3101, D.3107, E.3108 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:R.3094, B:D.3101, B:D.3107, B:E.3108, B:E.3108 CA.22: 7 residues within 4Å: Chain B: D.3154, I.3155, E.3157, N.3171, V.3172, G.3174, S.3175 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3154, B:I.3155, B:E.3157, B:V.3172, B:S.3175 CA.23: 3 residues within 4Å: Chain B: A.3291, D.3294, E.3323 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.3291, B:D.3294, B:E.3323 CA.24: 3 residues within 4Å: Chain B: V.3344, E.3367, T.3684 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:V.3344, B:E.3367 CA.25: 3 residues within 4Å: Chain B: A.3386, H.3387, P.3410 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.3386, B:P.3410 CA.26: 6 residues within 4Å: Chain B: W.3532, D.3535, Q.3537, D.3539, D.3545, E.3546 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3535, B:Q.3537, B:D.3539, B:D.3545, B:E.3546 CA.27: 7 residues within 4Å: Chain B: A.3572, C.3574, N.3575, R.3577, D.3579, D.3585, E.3586 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:A.3572, B:R.3577, B:D.3579, B:D.3585, B:E.3586 CA.28: 7 residues within 4Å: Chain B: W.3613, C.3615, D.3616, V.3618, D.3620, D.3626, E.3627 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3613, B:D.3616, B:V.3618, B:D.3620, B:D.3626 CA.29: 6 residues within 4Å: Chain B: W.3654, D.3657, D.3659, D.3661, D.3667, E.3668 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.3657, B:D.3659, B:D.3661, B:D.3667, B:E.3668 CA.30: 6 residues within 4Å: Chain B: A.3699, N.3702, F.3704, D.3706, D.3712, E.3713 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:A.3699, B:F.3704, B:D.3706, B:D.3712, B:E.3713 CA.31: 6 residues within 4Å: Chain B: W.3739, D.3742, T.3744, D.3746, D.3752, E.3753 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3739, B:D.3742, B:T.3744, B:D.3746, B:E.3753 CA.32: 6 residues within 4Å: Chain B: W.3778, D.3781, E.3783, D.3785, D.3791, E.3792 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3778, B:D.3781, B:E.3783, B:D.3791, B:E.3792 CA.33: 7 residues within 4Å: Chain B: L.3817, A.3818, D.3820, R.3822, D.3824, D.3830, E.3831 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:L.3817, B:R.3822, B:D.3824, B:D.3830, B:E.3831 CA.34: 8 residues within 4Å: Chain B: W.3861, I.3862, C.3863, D.3864, E.3866, D.3868, D.3874, E.3875 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3861, B:D.3864, B:D.3868, B:D.3874, B:E.3875 CA.35: 8 residues within 4Å: Chain B: Q.3903, L.3904, C.3905, N.3906, V.3908, D.3910, D.3916, E.3917 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Q.3903, B:V.3908, B:D.3916, B:D.3916, B:E.3917

Links

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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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