SMTL ID : 6tp5.1

Crystal structure of human Transmembrane prolyl 4-hydroxylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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.1: 3 residues within 4Å: Chain A: N.287, Q.333, Q.334 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.333 NAG-NAG.3: 3 residues within 4Å: Chain B: N.287, Q.333, Q.334 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN-MAN.2: 10 residues within 4Å: Chain A: N.119, V.298, N.301, R.302, T.303, Y.304, D.305, M.307, S.308, L.309 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- BMA- MAN- MAN- MAN- MAN: beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-BMA-MAN-MAN-MAN-MAN.4: 9 residues within 4Å: Chain B: V.298, N.301, R.302, T.303, Y.304, D.305, M.307, S.308, L.309 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.308

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.5: 12 residues within 4Å: Chain A: Y.238, Y.244, H.247, D.249, T.294, H.360, G.361, G.362, K.370, N.374, W.376 Ligands: FE2.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.238, A:N.374 Salt bridges: A:K.370 OGA.17: 12 residues within 4Å: Chain B: Y.238, Y.244, H.247, D.249, T.294, H.360, G.361, G.362, K.370, N.374, W.376 Ligands: FE2.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.238, B:T.294 Water bridges: B:K.370 Salt bridges: B:K.370

2 x FE2: FE (II) ION(Non-covalent)

FE2.6: 4 residues within 4Å: Chain A: H.247, D.249, H.360 Ligands: OGA.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.247, A:D.249, A:H.360 FE2.18: 4 residues within 4Å: Chain B: H.247, D.249, H.360 Ligands: OGA.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.247, B:D.249, B:H.360

8 x TBU: TERTIARY-BUTYL ALCOHOL(Non-functional Binders)

TBU.7: 3 residues within 4Å: Chain A: L.112, L.135, F.176 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.112, A:L.135, A:F.176, A:F.176 TBU.8: 4 residues within 4Å: Chain A: G.136, M.141, S.145, M.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.145 TBU.9: 2 residues within 4Å: Chain A: E.306, R.317 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.317 TBU.10: 2 residues within 4Å: Chain A: E.148 Chain B: N.286 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.286 Hydrogen bonds: A:E.148 TBU.19: 2 residues within 4Å: Chain A: N.286 Chain B: E.148 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.148 Hydrogen bonds: A:N.286 TBU.20: 7 residues within 4Å: Chain B: G.136, W.140, M.141, S.145, I.146, Y.179, M.180 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.179 TBU.21: 5 residues within 4Å: Chain B: L.112, L.135, F.168, M.171, F.176 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.112, B:F.168, B:F.176 TBU.22: 4 residues within 4Å: Chain B: Y.304, E.306, R.317, L.359 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.359 Hydrogen bonds: B:R.317

2 x GLY: GLYCINE(Non-covalent)

GLY.11: 1 residues within 4Å: Chain A: T.366 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.366 Salt bridges: A:R.367 GLY.12: 1 residues within 4Å: Chain A: D.121 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.121, G.12, G.12 Salt bridges: A:H.123

4 x CA: CALCIUM ION(Non-covalent)

CA.13: 6 residues within 4Å: Chain A: D.117, N.119, D.121, H.123, Q.125, E.128 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.117, A:D.121, A:H.123, A:E.128, A:E.128 CA.14: 5 residues within 4Å: Chain A: D.156, D.158, D.160, V.162, E.167 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.156, A:D.160, A:V.162, A:E.167, H2O.2 CA.23: 6 residues within 4Å: Chain B: D.117, N.119, D.121, H.123, Q.125, E.128 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.117, B:D.121, B:H.123, B:E.128, B:E.128 CA.24: 5 residues within 4Å: Chain B: D.156, D.158, D.160, V.162, E.167 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.156, B:D.158, B:D.160, B:V.162, B:E.167

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

CL.15: 3 residues within 4Å: Chain A: E.34, G.35, I.36 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: R.89, E.186, S.187 Chain B: R.89, S.187 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Myllykoski, M. et al., Structure of transmembrane prolyl 4-hydroxylase reveals unique organization of EF and dioxygenase domains. J.Biol.Chem. (2020)

Release Date

2020-12-23

Peptides

Transmembrane prolyl 4-hydroxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transmembrane prolyl 4-hydroxylase