SMTL ID : 8c6i.1

TMEM2 ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

monomer

Ligands

2 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.1: 5 residues within 4Å: Chain A: R.1116, Q.1117, Y.1128, N.1152, P.1174 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.3: 5 residues within 4Å: Chain A: Q.1009, N.1010, S.1012, K.1015, Q.1065 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.1015, A:Q.1065

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.2: 5 residues within 4Å: Chain A: H.797, R.830, N.832, H.869, H.1059 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: K.442, N.443 No protein-ligand interaction detected (PLIP)

1 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.4: 7 residues within 4Å: Chain A: N.166, S.167, P.171, F.172, G.173, Y.756, K.774 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: 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-FUC.5: 4 residues within 4Å: Chain A: N.996, D.1077, K.1079, D.1080 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.1079, A:K.1079

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.6: 5 residues within 4Å: Chain A: G.615, E.616, S.618, T.655, N.657 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.616, A:E.616, A:S.618

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

NI.8: 3 residues within 4Å: Chain A: H.468, H.470, H.503 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.468, A:H.470, A:H.503

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

CL.9: 2 residues within 4Å: Chain A: F.1156, K.1180 Ligand excluded by PLIP

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

NAG.10: 2 residues within 4Å: Chain A: Q.1215, N.1217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.1215 NAG.11: 2 residues within 4Å: Chain A: Y.889, N.898 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.889, A:N.898

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, M. et al., Structure of the transmembrane protein 2 (TMEM2) ectodomain and its apparent lack of hyaluronidase activity. Wellcome Open Res (2023)

Release Date

2023-02-01

Peptides

Cell surface hyaluronidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cell surface hyaluronidase