SMTL ID : 6vlr.1

BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-1-1-mer

Ligands

8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 2 residues within 4Å: Chain A: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: Q.263, I.264, N.265, N.301, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: Q.263, N.265, N.301, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain D: K.122, E.123, S.125, N.126 No protein-ligand interaction detected (PLIP)

4 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.3: 8 residues within 4Å: Chain A: P.182, K.222, V.224, L.231, N.232, V.414, S.415 Ligands: NAG.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.414 Hydrogen bonds: A:V.414 NAG-NAG-BMA-MAN-MAN.7: 11 residues within 4Å: Chain A: N.107, I.108 Chain G: Y.33, G.55, D.56, N.58, H.100, R.102, F.114 Chain H: D.87, T.92 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:N.58 Hydrogen bonds: G:N.58, G:Y.33, G:Y.33, G:H.100 NAG-NAG-BMA-MAN-MAN.11: 8 residues within 4Å: Chain C: E.181, N.232, F.345, N.346, C.347, C.413, V.414, S.415 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.414 Hydrogen bonds: C:V.414 NAG-NAG-BMA-MAN-MAN.17: 8 residues within 4Å: Chain E: E.181, L.231, N.232, G.348, C.413, V.414, S.415 Ligands: NAG.34 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.414 Hydrogen bonds: E:G.348, E:V.414

2 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.5: 5 residues within 4Å: Chain A: N.118, C.119, S.120, Y.135, D.290 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.135 NAG-NAG-BMA.12: 5 residues within 4Å: Chain C: N.118, C.119, S.120, Y.135, D.290 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C: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.6: 15 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, S.381, T.383 Chain G: R.103, I.104, G.106, V.107, V.108 Chain H: N.42, N.43, P.58, S.60 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.108 NAG-NAG-BMA-MAN-MAN-MAN.13: 14 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, S.381 Chain I: R.103, I.104, G.106, V.107, V.108 Chain J: N.42, N.43, P.58, S.60 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.108 NAG-NAG-BMA-MAN-MAN-MAN.18: 15 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, S.381, T.383 Chain K: R.103, I.104, G.106, V.107, V.108 Chain L: N.42, N.43, P.58, S.60 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:V.108

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.14: 14 residues within 4Å: Chain C: N.107, I.108 Chain I: Y.33, S.54, G.55, D.56, N.58, W.113, F.114, T.115 Chain J: W.86, D.87, S.88, T.92 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.58, I:Y.33, I:Y.33 NAG-NAG-BMA-MAN.19: 9 residues within 4Å: Chain E: N.107, I.108 Chain K: S.54, D.56, N.58, F.114, T.115 Chain L: D.87, T.92 No protein-ligand interaction detected (PLIP)

24 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.20: 4 residues within 4Å: Chain A: V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.3 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: F.203, N.204, T.206 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: F.121, N.122, K.133 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG.8 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: C.101, T.102, N.103, K.117, Y.161 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: E.57, N.58 Chain D: G.16, S.17 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain C: N.232, Q.263, V.414, S.415, N.416 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: F.203, N.204, T.206 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: F.121, N.122, K.133 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.271, I.292, V.410 Chain J: F.62 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain C: V.144, R.162, L.163, I.164, N.167 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.361 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain C: S.333, T.341, T.342, N.355, S.357 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, S.17 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain E: P.261, V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.17 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain E: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain E: F.203, N.204, G.205, T.206, G.207, P.208 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: F.121, N.122, K.133 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: N.271, I.292, V.410 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain E: N.355, S.357 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167, T.168 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain E: T.102, N.103 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain E: V.104, N.118, Y.135, L.137, G.289, D.290 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain F: N.126 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 gp120: ACE
BG505 SOSIPv5.2 gp41: BDF
PGT122 Fab Heavy Chain: GIK
PGT122 Fab Light Chain: HJL
RM20E1 Fab Heavy Chain: M
RM20E1 Fab Kappa Chain: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
H

E
G

B
B

D
J

F
I

G
C

I
D

K
E

H
L

J
K

L
M

M
F

N
N

Envelope glycoprotein gp120

BG505 SOSIPv5.2 gp41

PGT122 Fab Heavy Chain

PGT122 Fab Light Chain

RM20E1 Fab Heavy Chain

RM20E1 Fab Kappa Chain

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