SMTL ID : 6vn0.1

BG505 SOSIP.v4.1 in complex with rhesus macaque Fab RM20F

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

6 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: 9 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, D.113 Chain C: G.55, G.56, T.57, Y.59, T.68 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.59 Hydrogen bonds: C:Y.59 NAG-NAG-BMA-MAN-MAN.5: 9 residues within 4Å: Chain A: S.179, P.182, V.224, L.231, N.232, Q.408, C.413, V.414, S.415 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.408, A:V.414 Hydrophobic interactions: A:V.414 NAG-NAG-BMA-MAN-MAN.12: 9 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, D.113 Chain G: G.55, G.56, T.57, Y.59, T.68 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Y.59 Hydrogen bonds: G:Y.59 NAG-NAG-BMA-MAN-MAN.16: 9 residues within 4Å: Chain E: S.179, P.182, V.224, L.231, N.232, Q.408, C.413, V.414, S.415 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.408, E:V.414 Hydrophobic interactions: E:V.414 NAG-NAG-BMA-MAN-MAN.23: 9 residues within 4Å: Chain I: E.57, N.58 Chain J: G.16, D.113 Chain K: G.55, G.56, T.57, Y.59, T.68 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:Y.59 Hydrogen bonds: K:Y.59 NAG-NAG-BMA-MAN-MAN.27: 9 residues within 4Å: Chain I: S.179, P.182, V.224, L.231, N.232, Q.408, C.413, V.414, S.415 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Q.408, I:V.414 Hydrophobic interactions: I:V.414

27 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: 6 residues within 4Å: Chain A: V.104, N.106, N.118, Y.135, L.137, D.290 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.135 Hydrogen bonds: A:Y.135 NAG-NAG.3: 2 residues within 4Å: Chain A: F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: W.66, N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: N.265, T.267, H.299, C.300, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.332, S.333, T.341, N.355, S.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332 NAG-NAG.9: 3 residues within 4Å: Chain A: S.357, G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: R.162, N.167, T.168 Chain I: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: V.414, S.415, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain E: V.104, N.106, N.118, Y.135, L.137, D.290 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.135 Hydrogen bonds: E:Y.135 NAG-NAG.14: 2 residues within 4Å: Chain E: F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: W.66, N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain E: N.265, T.267, H.299, C.300, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain E: N.332, S.333, T.341, N.355, S.357 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.332 NAG-NAG.20: 3 residues within 4Å: Chain E: S.357, G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain E: V.414, S.415, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain I: V.104, N.106, N.118, Y.135, L.137, D.290 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.135 Hydrogen bonds: I:Y.135 NAG-NAG.25: 2 residues within 4Å: Chain I: F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain I: W.66, N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain I: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain I: N.265, T.267, H.299, C.300, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain I: N.332, S.333, T.341, N.355, S.357 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.332 NAG-NAG.31: 3 residues within 4Å: Chain I: S.357, G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain E: R.278 Chain I: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain I: V.414, S.415, N.416 No protein-ligand interaction detected (PLIP)

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

NAG.34: 5 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.324, N.325 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: C.101, T.102, N.103, K.117, Y.161 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.105, R.106, N.107 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: S.125, N.126 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: P.98, W.99, N.100 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain E: Q.263, N.265, N.301, V.302, S.303 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: N.324, N.325 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain E: C.101, T.102, N.103, K.117, Y.161 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain E: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain F: N.105, R.106, N.107 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain F: S.125, N.126 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain F: P.98, W.99, N.100 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain I: Q.263, N.265, N.301, V.302, S.303 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain I: N.324, N.325 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain I: C.101, T.102, N.103, K.117, Y.161 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain I: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain J: N.105, R.106, N.107 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain J: S.125, N.126 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain J: P.98, W.99, N.100 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, C.A. et al., Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates. Plos Pathog. (2020)

Release Date

2020-06-24

Peptides

Envelope glycoprotein gp160: AEI
Envelope glycoprotein gp41: BFJ
RM20F Fab Heavy Chain: CGK
RM20F Kappa Chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
D

B
B

F
E

J
F

C
H

G
G

K
I

D
L

H
J

L
K

Envelope glycoprotein gp160

Envelope glycoprotein gp41

RM20F Fab Heavy Chain

RM20F Kappa Chain

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