SMTL ID : 9nnd.1

Structure of the HERV-K (HML-2) spike complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

15 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: 6 residues within 4Å: Chain A: M.10, T.18, D.38, K.41, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.34, N.89 Chain B: R.352 Chain C: H.139 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: M.62, I.63, N.64, E.317, N.318 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: H.215, N.266, D.281, N.283 Ligands: NAG-NAG.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.215 NAG-NAG.7: 7 residues within 4Å: Chain B: I.262, W.263, S.264, N.283, S.284, S.285 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: T.18, D.38, K.41, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.34, N.89 Chain D: H.139 Chain E: R.352 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain D: M.10, T.18, D.38, K.41, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: H.139 Chain D: N.34, W.88, N.89 Chain F: R.352 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain E: M.62, I.63, N.64, E.317, N.318 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain E: H.215, N.266, N.283 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 8 residues within 4Å: Chain E: I.262, W.263, S.264, N.283, S.284, S.285 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain F: M.62, I.63, N.64, E.317, N.318 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain F: H.215, N.266, N.283 Ligands: NAG-NAG.21 1 PLIP interactions: 1 interactions with chain F Water bridges: F:H.215 NAG-NAG.21: 7 residues within 4Å: Chain F: I.262, S.264, N.283, S.284, S.285 Ligands: NAG-NAG.20, NAG-NAG.20 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.3: 3 residues within 4Å: Chain A: N.101, S.103, E.104 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.10: 3 residues within 4Å: Chain C: N.101, S.103, E.104 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.13: 3 residues within 4Å: Chain D: N.101, S.103, E.104 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: 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.4: 8 residues within 4Å: Chain B: N.39, H.259, P.289, L.290, Q.291, D.326, S.327, T.328 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.328 Hydrogen bonds: B:S.327 Water bridges: B:S.327 NAG-NAG-BMA-MAN-MAN.14: 8 residues within 4Å: Chain E: N.39, D.40, H.259, P.289, Q.291, D.326, S.327, T.328 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:T.328 Hydrogen bonds: E:S.327 Water bridges: E:S.327 NAG-NAG-BMA-MAN-MAN.18: 9 residues within 4Å: Chain F: N.39, D.40, H.259, P.289, L.290, Q.291, D.326, S.327, T.328 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.328 Hydrogen bonds: F:S.327 Water bridges: F:S.327

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

NAG.22: 2 residues within 4Å: Chain A: N.120, L.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.120 NAG.23: 2 residues within 4Å: Chain B: N.185, S.187 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain C: N.120, L.121 No protein-ligand interaction detected (PLIP) NAG.25: 2 residues within 4Å: Chain D: N.120, L.121 No protein-ligand interaction detected (PLIP) NAG.26: 2 residues within 4Å: Chain E: N.185, S.187 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.187 NAG.27: 2 residues within 4Å: Chain F: N.185, S.187 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaked, R. et al., The prefusion structure of the HERV-K spike complex. To Be Published

Release Date

2025-07-02

Peptides

Endogenous retrovirus group K member 7 Pol protein: ACD
Surface protein: BEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

C
c

D
b

B
A

E
B

F
C

Endogenous retrovirus group K member 7 Pol protein

Surface protein