SMTL ID : 7uoj.1

The CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP.664

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-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: 2 residues within 4Å: Chain A: N.118, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: Q.100, S.120, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.265, V.302, S.303, S.381 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.271, I.292 Chain E: F.65 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG-BMA.6, NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: L.235, P.261, Q.263, N.416 Ligands: NAG-NAG-BMA-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: N.246 Chain D: H.24, I.26, R.60, Y.85 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.60, D:R.60 NAG-NAG.12: 3 residues within 4Å: Chain G: N.118, D.290 Chain K: R.92 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain G: T.98, Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain G: N.265, N.301, S.381, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain G: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain G: S.357, N.361 Ligands: NAG-NAG-BMA.17, NAG-NAG-BMA-MAN-MAN.18, NAG-NAG-BMA-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain G: L.235, P.261, Q.263, N.416 Ligands: NAG-NAG-BMA-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain G: N.246 Chain J: H.24, I.25, I.26, R.60, Y.85 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:I.25, J:R.60, J:R.60, J:Y.85 NAG-NAG.23: 3 residues within 4Å: Chain M: N.118, D.290 Chain Q: R.92 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain M: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain M: N.265, N.301, S.381, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain M: N.271, I.292 Chain Q: F.65 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:F.65 NAG-NAG.30: 4 residues within 4Å: Chain M: N.361 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA-MAN-MAN.29, NAG-NAG-BMA-MAN-MAN.29 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 5 residues within 4Å: Chain M: L.235, P.261, Q.263, N.416 Ligands: NAG-NAG-BMA-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain M: N.246 Chain P: H.24, I.25, I.26, R.60 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:R.60, P:R.60

3 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.3: 8 residues within 4Å: Chain A: E.181, P.182, V.224, N.232, G.348, V.414, S.415 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN.14: 10 residues within 4Å: Chain G: S.179, E.181, P.182, V.224, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.21 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.348, G:S.179, G:S.179 NAG-NAG-BMA-MAN.25: 10 residues within 4Å: Chain M: S.179, E.181, P.182, V.224, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.32 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:G.348, M:S.179, M:S.179

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.6: 6 residues within 4Å: Chain A: N.332, S.333, T.341 Ligands: NAG-NAG-BMA-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN.7, NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 6 residues within 4Å: Chain G: N.332, S.333, T.341 Ligands: NAG-NAG-BMA-MAN-MAN.18, NAG-NAG-BMA-MAN-MAN.18, NAG-NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 5 residues within 4Å: Chain M: N.332, S.333, T.341 Ligands: NAG-NAG-BMA-MAN-MAN.29, NAG-NAG.30 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.7: 9 residues within 4Å: Chain A: D.111, N.355, S.357, G.358, P.385 Ligands: NAG-NAG-BMA.6, NAG-NAG-BMA.6, NAG-NAG-BMA.6, NAG-NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.111 NAG-NAG-BMA-MAN-MAN.18: 8 residues within 4Å: Chain G: D.111, N.355, S.357, P.385 Ligands: NAG-NAG-BMA.17, NAG-NAG-BMA.17, NAG-NAG.19, NAG-NAG.19 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.111 NAG-NAG-BMA-MAN-MAN.29: 8 residues within 4Å: Chain M: N.355, S.357, G.358, P.385 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA.28, NAG-NAG.30, NAG-NAG.30 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:S.357

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.9: 12 residues within 4Å: Chain A: T.267, H.299, N.301 Chain E: N.46, Q.47, P.61, S.63 Chain F: R.102, R.103, I.104, G.106, I.107 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.20: 12 residues within 4Å: Chain G: N.265, T.267, H.299, N.301 Chain K: N.45, N.46, Q.47, S.63 Chain L: R.103, I.104, G.106, I.107 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.31: 12 residues within 4Å: Chain M: N.265, T.267, H.299, N.301 Chain Q: N.45, N.46, Q.47, S.63 Chain R: R.103, I.104, G.106, I.107 No protein-ligand interaction detected (PLIP)

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

NAG.34: 2 residues within 4Å: Chain A: N.58 Chain B: N.114 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: R.162, N.167, T.168 Chain C: Q.76 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: N.204, T.206, P.208, E.245 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: K.304, N.308 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.58 Chain H: N.114 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain G: N.103, K.117 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain G: R.162, N.167, T.168 Chain I: Q.76 Chain M: E.126 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: N.204, T.206, P.208 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: N.308, S.362, W.364 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain M: N.58 Chain N: T.18, N.114 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain M: N.103, K.117 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain M: R.162, N.167, T.168 Chain O: Q.76 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain M: N.204, E.245 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain M: N.308, W.364 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, D.N. et al., The structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP. To Be Published

Release Date

2023-05-03

Peptides

Envelope glycoprotein gp120: AGM
Envelope glycoprotein gp41: BHN
N49-P9.6-FR3 Fab heavy chain: CIO
N49-P9.6-FR3 Fab light chain: DJP
PGT121 Fab light chain: EKQ
PGT121 Fab heavy chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

G
A

M
I

B
B

H
C

N
J

C
H

I
D

O
K

D
L

J
E

P
M

E
l

K
e

Q
m

F
h

L
d

R
k

Envelope glycoprotein gp120

Envelope glycoprotein gp41

N49-P9.6-FR3 Fab heavy chain

N49-P9.6-FR3 Fab light chain

PGT121 Fab light chain

PGT121 Fab heavy chain

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