SMTL ID : 6thg.1

Cedar Virus attachment glycoprotein (G) in complex with human ephrin-B1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.07 Å

Oligo State

hetero-5-5-mer

Ligands

6 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: 5 residues within 4Å: Chain A: D.123, N.124, I.160, N.220, R.223 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 8 residues within 4Å: Chain A: K.8, S.9, V.10, N.357, T.359, T.360, L.362 Chain G: K.30 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.30 NAG-NAG-BMA.4: 5 residues within 4Å: Chain C: D.123, I.160, N.185, N.220, R.223 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 8 residues within 4Å: Chain B: K.30 Chain C: K.8, S.9, V.10, N.357, T.359, T.360, L.362 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.30 NAG-NAG-BMA.7: 4 residues within 4Å: Chain D: D.123, N.124, N.220 Chain F: Q.29 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:Q.29, D:N.124 NAG-NAG-BMA.11: 3 residues within 4Å: Chain E: N.294, N.297, D.335 No protein-ligand interaction detected (PLIP)

7 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: 3 residues within 4Å: Chain A: N.294, W.295, N.297 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain D: Q.96, I.115, N.117, E.131 Chain I: K.23, V.26 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: E.286, N.294, W.295, N.297 Chain F: Y.79 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.286 NAG-NAG.9: 4 residues within 4Å: Chain D: V.10, K.334, N.357, T.360 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain D: N.236 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain F: D.123, N.124, N.185, N.220, S.222, R.223 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.185 NAG-NAG.13: 4 residues within 4Å: Chain G: N.114, S.116, E.118, G.119 No protein-ligand interaction detected (PLIP)

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

NAG.14: 3 residues within 4Å: Chain A: N.106, G.173, E.174 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.117, E.131, Y.133 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.236 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.114, S.116, E.118, G.119 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain C: N.106, G.173, E.174, Q.234 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: N.297, T.299 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.152, D.239, F.240 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.198 Ligand excluded by PLIP NAG.22: 7 residues within 4Å: Chain D: C.105, N.106, C.171, G.173, E.174, F.176, Q.234 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain E: D.123, N.124, I.160, N.185, N.220 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain E: V.10, N.357, T.360 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain E: D.44, C.105, N.106, G.173, E.174 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain F: C.105, N.106, G.173, E.174 Ligand excluded by PLIP NAG.27: 7 residues within 4Å: Chain F: K.8, S.9, V.10, N.357, T.359, T.360, L.362 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain H: N.114, E.118, G.119 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain I: N.114, S.116, E.118, G.119 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain J: N.114, S.116, E.118, G.119 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pryce, R. et al., A key region of molecular specificity orchestrates unique ephrin-B1 utilization by Cedar virus. Life Sci Alliance (2020)

Release Date

2019-12-18

Peptides

Attachment glycoprotein: ACDEF
Ephrin-B1: BGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
A

D
E

E
G

F
I

B
D

G
C

H
F

I
H

J
J

Attachment glycoprotein

Ephrin-B1

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