SMTL ID : 6u7n.1

Crystal structure of neurotrimin (NTM)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.32 Å

Oligo State

homo-dimer

Ligands

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.1: 11 residues within 4Å: Chain A: N.65, R.66, T.68, D.80, R.82, V.83, I.97, D.101, Y.103, D.104, Y.108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 11 residues within 4Å: Chain B: N.65, R.66, T.68, D.80, R.82, V.83, I.97, D.101, Y.103, D.104, Y.108 No protein-ligand interaction detected (PLIP)

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 6 residues within 4Å: Chain A: G.145, N.146, N.147, E.182, Q.184, G.185 No protein-ligand interaction detected (PLIP) NAG-FUC.15: 6 residues within 4Å: Chain B: G.145, N.146, N.147, E.182, Q.184, G.185 No protein-ligand interaction detected (PLIP)

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: E.144, R.188, Y.216, Y.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.144, A:R.188 EDO.4: 6 residues within 4Å: Chain A: H.166, A.171, V.172, G.173, F.174, V.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.166, A:V.172, A:G.173 EDO.5: 5 residues within 4Å: Chain A: T.213, N.215, V.243, P.244, S.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.245, A:S.245 EDO.16: 4 residues within 4Å: Chain B: E.144, R.188, Y.216, Y.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.144, B:R.188 EDO.17: 6 residues within 4Å: Chain B: H.166, A.171, V.172, G.173, F.174, V.175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.166, B:V.172, B:G.173 EDO.18: 5 residues within 4Å: Chain B: T.213, N.215, V.243, P.244, S.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.245, B:S.245

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

CL.6: 3 residues within 4Å: Chain A: K.132, I.133, V.206 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.208, R.209 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Y.219, S.221 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: A.242, S.245, P.270, F.271 Chain B: V.172 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: S.141, I.142, N.215, K.295 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: R.165, I.167, R.209 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: R.188, S.191, V.214, Y.216, V.243 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: P.244, N.294, K.295 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: K.132, I.133, V.206 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: R.208, R.209 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: Y.219, S.221 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain A: V.172 Chain B: A.242, S.245, P.270, F.271 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: S.141, I.142, N.215, K.295 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: R.165, I.167, R.209 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain B: R.188, S.191, V.214, Y.216, V.243 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: P.244, N.294, K.295 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venkannagari, H. et al., Highly Conserved Molecular Features in IgLONs Contrast Their Distinct Structural and Biological Outcomes. J.Mol.Biol. (2020)

Release Date

2020-08-12

Peptides

Neurotrimin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Neurotrimin