SMTL ID : 6fj3.1

High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN-MAN-FUC.1: 6 residues within 4Å: Chain A: L.91, N.96, R.97, T.98 Chain B: Y.34 Ligands: MAN.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.91 Hydrogen bonds: A:T.98, A:T.98, B:Y.34

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

NAG-NAG-BMA-FUC.2: 6 residues within 4Å: Chain A: Y.80, W.99, N.101, S.103, E.104, K.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.80, A:E.104 Hydrophobic interactions: A:K.107

1 x NAG- NAG- BMA- MAN: 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.3: 5 residues within 4Å: Chain A: D.84, R.85, N.86 Ligands: MAN.5, MAN.6 No protein-ligand interaction detected (PLIP)

3 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.4: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1, NAG-NAG-BMA-MAN-MAN-FUC.1 No protein-ligand interaction detected (PLIP) MAN.5: 3 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.3, NAG-NAG-BMA-MAN.3, MAN.6 No protein-ligand interaction detected (PLIP) MAN.6: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.3, MAN.5 No protein-ligand interaction detected (PLIP)

9 x OLA: OLEIC ACID(Non-covalent)

OLA.7: 6 residues within 4Å: Chain A: H.242, S.243, Y.255, G.258, F.259 Ligands: OLA.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.259 Salt bridges: A:H.242, A:K.247 OLA.8: 5 residues within 4Å: Chain A: Y.156, H.160, L.256, T.260 Ligands: OLA.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.156, A:Y.156, A:L.256 Salt bridges: A:H.160 OLA.9: 1 residues within 4Å: Chain A: T.322 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.322 OLA.10: 6 residues within 4Å: Chain A: L.533, P.537, L.538, V.541, H.542, Y.565 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.537, A:V.541, A:Y.565 Salt bridges: A:K.530 OLA.11: 5 residues within 4Å: Chain A: S.531, L.538, A.580, C.584, Q.589 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.538 Hydrogen bonds: A:Q.589 OLA.12: 2 residues within 4Å: Chain A: A.304, L.308 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.304, A:L.308 OLA.13: 3 residues within 4Å: Chain A: L.308, I.311 Ligands: OLA.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.308, A:I.311 OLA.14: 5 residues within 4Å: Chain A: H.151, Y.156, M.159, L.163 Ligands: OLA.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.159, A:L.163 OLA.15: 5 residues within 4Å: Chain A: W.596, W.599, T.600, L.601, A.602 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.596, A:T.600, A:A.602

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.16: 1 residues within 4Å: Chain A: H.75 No protein-ligand interaction detected (PLIP)

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

PG4.17: 5 residues within 4Å: Chain A: T.474, N.475, E.476, L.480 Ligands: CL.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.475, A:N.475

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

CL.18: 3 residues within 4Å: Chain A: R.470, I.473 Ligands: PG4.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehrenmann, J. et al., High-resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-11-21

Peptides

Parathyroid hormone/parathyroid hormone-related peptide receptor,Parathyroid hormone/parathyroid hormone-related peptide receptor,GlgA glycogen synthase,Parathyroid hormone/parathyroid hormone-related peptide receptor: A
Parathyroid hormone: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Parathyroid hormone/parathyroid hormone-related peptide receptor,Parathyroid hormone/parathyroid hormone-related peptide receptor,GlgA glycogen synthase,Parathyroid hormone/parathyroid hormone-related peptide receptor

Parathyroid hormone