SMTL ID : 7lg6.1

BG505 SOSIP.v5.2 in complex with VRC40.01 and RM19R Fabs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

30 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: 3 residues within 4Å: Chain A: E.57, N.58 Chain D: 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: 3 residues within 4Å: Chain A: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.10, NAG-NAG.13, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain A: N.332, S.333, T.341 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain G: E.57, N.58 Chain J: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain G: S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain G: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain G: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain G: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG.24, NAG-NAG.27, NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain G: S.357, N.361 Ligands: NAG-NAG.23, NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain G: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain G: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain G: N.332, S.333, T.341 Ligands: NAG-NAG.23, NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain M: E.57, N.58 Chain P: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain M: S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain M: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 6 residues within 4Å: Chain M: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 5 residues within 4Å: Chain M: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 5 residues within 4Å: Chain M: N.355, S.357 Ligands: NAG-NAG.38, NAG-NAG.41, NAG-NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain M: S.357, N.361 Ligands: NAG-NAG.37, NAG-NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain M: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 3 residues within 4Å: Chain M: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 5 residues within 4Å: Chain M: N.332, S.333, T.341 Ligands: NAG-NAG.37, NAG-NAG.37 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.16: 6 residues within 4Å: Chain G: V.104, N.106, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.135 NAG-NAG-BMA.30: 6 residues within 4Å: Chain M: V.104, N.106, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M: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: 11 residues within 4Å: Chain A: S.179, E.181, P.182, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.414 NAG-NAG-BMA-MAN-MAN-MAN.19: 11 residues within 4Å: Chain G: S.179, E.181, P.182, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.25 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.414 NAG-NAG-BMA-MAN-MAN-MAN.33: 11 residues within 4Å: Chain M: S.179, E.181, P.182, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.39 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:V.414

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: 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.6: 13 residues within 4Å: Chain A: N.246, T.248, N.249 Chain B: G.107, F.108, A.110 Chain C: D.30, S.32, Y.49, S.53, R.54, I.56, Y.92 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.107, C:S.53, C:S.53, B:A.110, C:D.30, C:S.32 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.20: 13 residues within 4Å: Chain G: N.246, T.248, N.249 Chain H: G.107, F.108, A.110 Chain I: D.30, S.32, Y.49, S.53, R.54, I.56, Y.92 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:G.107, I:S.53, I:S.53, H:A.110, I:D.30, I:S.32 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.34: 13 residues within 4Å: Chain M: N.246, T.248, N.249 Chain N: G.107, F.108, A.110 Chain O: D.30, S.32, Y.49, S.53, R.54, I.56, Y.92 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain O Hydrogen bonds: N:G.107, O:S.53, O:S.53, N:A.110, O:D.30, O:S.32

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.14: 6 residues within 4Å: Chain D: P.98, N.100, S.102, W.103, Y.127, L.134 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.98, D:Y.127 NAG-FUC.28: 6 residues within 4Å: Chain J: P.98, N.100, S.102, W.103, Y.127, L.134 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:P.98, J:Y.127 NAG-FUC.42: 6 residues within 4Å: Chain P: P.98, N.100, S.102, W.103, Y.127, L.134 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:P.98, P:Y.127

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

NAG.43: 4 residues within 4Å: Chain A: R.162, N.167 Chain G: E.126, R.278 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: K.304, N.308, W.364 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain A: N.103, T.105, K.117 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain A: N.107 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain D: N.107, S.109 Chain E: T.56 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: E.123, N.126 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain G: R.162, N.167 Chain M: E.126, R.278 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain G: K.304, N.308, W.364 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain G: N.103, T.105, K.117 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain G: N.107 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain J: N.107, S.109 Chain K: T.56 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain J: E.123, N.126 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain A: E.126, R.278 Chain M: R.162, N.167 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain M: K.304, N.308, W.364 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain M: N.103, T.105, K.117 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain M: N.107 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain P: N.107, S.109 Chain Q: T.56 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain P: E.123, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, C.A. et al., Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies. Cell Rep (2021)

Release Date

2021-09-15

Peptides

Envelope glycoprotein gp120: AGM
VRC40.01 Fab Heavy Chain: BHN
VRC40.01 Fab Kappa Light Chain: CIO
Envelope glycoprotein gp41: DJP
RM19R Fab Kappa Light Chain: EKQ
RM19R Fab Heavy Chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
E

M
F

B
H

H
O

N
P

C
L

I
Q

O
R

D
B

J
G

P
I

E
D

K
M

Q
N

F
C

L
J

R
K

Envelope glycoprotein gp120

VRC40.01 Fab Heavy Chain

VRC40.01 Fab Kappa Light Chain

Envelope glycoprotein gp41

RM19R Fab Kappa Light Chain

RM19R Fab Heavy Chain

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