SMTL ID : 6vo1.1

BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20J

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

21 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: 5 residues within 4Å: Chain A: E.57, N.58 Chain B: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.204, T.206, P.208, S.244 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.208 NAG-NAG.6: 2 residues within 4Å: Chain A: N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: S.357, G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: E.57, N.58 Chain F: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain E: S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: N.204, T.206, P.208, S.244 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.208 NAG-NAG.15: 2 residues within 4Å: Chain E: N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: S.357, G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain I: E.57, N.58 Chain J: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain I: S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain I: N.204, T.206, P.208, S.244 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:P.208 NAG-NAG.24: 2 residues within 4Å: Chain I: N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain I: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain I: S.357, G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain I: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.23 No protein-ligand interaction detected (PLIP)

3 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.2: 6 residues within 4Å: Chain A: V.104, N.106, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.135 NAG-NAG-BMA.11: 6 residues within 4Å: Chain E: V.104, N.106, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.135 NAG-NAG-BMA.20: 6 residues within 4Å: Chain I: V.104, N.106, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.135

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.5: 13 residues within 4Å: Chain A: S.179, P.182, V.224, L.231, N.232, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.348, A:V.414 NAG-NAG-BMA-MAN-MAN-MAN.14: 13 residues within 4Å: Chain E: S.179, P.182, V.224, L.231, N.232, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.18 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.348, E:V.414 NAG-NAG-BMA-MAN-MAN-MAN.23: 13 residues within 4Å: Chain I: S.179, P.182, V.224, L.231, N.232, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.27 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.348, I:V.414

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

NAG.28: 5 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: N.332, S.333, T.341, N.355, S.357 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: G.323, N.324 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: K.304, A.305, N.308 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.103, T.105, K.117 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: V.144, R.162, N.167 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain E: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain E: N.332, S.333, T.341, N.355, S.357 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: G.323, N.324 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: K.304, A.305, N.308 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: N.103, T.105, K.117 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain E: V.144, R.162, N.167 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain I: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain I: N.332, S.333, T.341, N.355, S.357 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain I: G.323, N.324 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain I: K.304, A.305, N.308 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain I: N.103, T.105, K.117 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain I: V.144, R.162, N.167 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

2020-07-01

Peptides

Envelope glycoprotein gp120: AEI
Envelope glycoprotein gp41: BFJ
RM20J Heavy chain Fab: CGK
RM20J Kappa light 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 gp120

Envelope glycoprotein gp41

RM20J Heavy chain Fab

RM20J Kappa light chain

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