SMTL ID : 9mla.1

Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 7 residues within 4Å: Chain A: N.32, D.33, H.252, P.282, L.283, Q.284, D.319 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.282 Hydrogen bonds: A:D.319 NAG-NAG-BMA-MAN-MAN.6: 6 residues within 4Å: Chain B: N.32, D.33, H.252, P.282, L.283, Q.284 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.282 NAG-NAG-BMA-MAN-MAN.11: 7 residues within 4Å: Chain C: N.32, D.33, H.252, P.282, L.283, Q.284, D.319 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.282 Hydrogen bonds: C:D.319

12 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: Y.176, N.178, S.180 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.94, N.259, D.274, N.276 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: I.255, W.256, S.257, N.276, S.277, S.278 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: M.55, N.57, E.310, N.311 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: K.133, Y.176, N.178, S.180 Chain H: Y.104 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: S.94, N.259, D.274, N.276 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain B: I.255, W.256, S.257, N.276, S.277, S.278 Ligands: NAG-NAG.8, NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.57, E.310, N.311 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: Y.176, N.178, S.180, E.218 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: S.94, N.259, D.274, N.276 Ligands: NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain C: I.255, W.256, S.257, N.276, S.277, S.278 Ligands: NAG-NAG.13, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.57, E.310, N.311 No protein-ligand interaction detected (PLIP)

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.16: 6 residues within 4Å: Chain D: I.9, M.10, T.18, D.38, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 5 residues within 4Å: Chain A: R.345 Chain D: N.34, W.88, N.89 Chain F: H.139 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 7 residues within 4Å: Chain E: I.9, M.10, T.18, A.19, D.38, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 5 residues within 4Å: Chain B: R.345 Chain D: H.139 Chain E: N.34, W.88, N.89 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 7 residues within 4Å: Chain F: I.9, M.10, T.18, A.19, D.38, N.42, R.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 5 residues within 4Å: Chain C: R.345 Chain E: H.139 Chain F: N.34, W.88, N.89 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- FUC: 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-FUC.18: 3 residues within 4Å: Chain D: N.101, S.103, E.104 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.104 NAG-NAG-BMA-FUC.21: 3 residues within 4Å: Chain E: N.101, S.103, E.104 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:E.104 NAG-NAG-BMA-FUC.24: 3 residues within 4Å: Chain F: N.101, S.103, E.104 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:E.104

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

NAG.25: 1 residues within 4Å: Chain A: N.4 No protein-ligand interaction detected (PLIP) NAG.26: 4 residues within 4Å: Chain B: N.4, T.6, S.342 Chain E: V.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.6, B:T.6, B:S.342 NAG.27: 2 residues within 4Å: Chain C: N.4, S.342 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.342 NAG.28: 2 residues within 4Å: Chain D: N.120, L.121 No protein-ligand interaction detected (PLIP) NAG.29: 2 residues within 4Å: Chain E: N.120, L.121 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain F: N.120, L.121 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shek, J. et al., Human endogenous retrovirus HERV-K envelope glycoprotein structures in pre- and post-fusion conformations by cryo-EM. To Be Published

Release Date

2025-07-30

Peptides

Surface protein: ABC
Transmembrane protein,Fibritin: DEF
Kenv-6 Fab heavy chain: GHI
Kenv-6 Fab light chain: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Surface protein

Transmembrane protein,Fibritin

Kenv-6 Fab heavy chain

Kenv-6 Fab light chain

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