SMTL ID : 9ogl.1

BG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

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

Ligands

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.1: 8 residues within 4Å: Chain J: Y.28, G.29, S.30, W.65, G.66, Y.89 Chain O: N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 10 residues within 4Å: Chain Q: E.181, P.182, V.224, L.231, N.232, N.346, C.413, V.414, S.415 Ligands: NAG.51 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:V.414

1 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.2: 14 residues within 4Å: Chain O: E.34, E.181, P.182, K.222, V.224, L.231, N.232, F.345, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.27 2 PLIP interactions: 2 interactions with chain O Hydrophobic interactions: O:V.414 Hydrogen bonds: O:V.414, O:E.34, O:E.34

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN.3: 23 residues within 4Å: Chain A: V.2, D.27, S.28, R.29, H.33, R.102, I.103, Y.104, G.105, V.106, V.107, F.113, D.118 Chain B: S.50, S.51, Q.52 Chain O: N.265, T.267, D.294, R.296, H.299, N.301, T.383 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.107 Hydrogen bonds: A:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10: 24 residues within 4Å: Chain C: V.2, D.27, S.28, R.29, H.33, R.98, R.102, I.103, Y.104, G.105, V.106, V.107, F.113 Chain D: S.50, S.51, Q.52 Chain P: N.265, T.267, D.294, R.296, H.299, N.301, T.383, R.412 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.107

2 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.4: 15 residues within 4Å: Chain A: S.34, D.51, H.53, N.55, A.57, T.58, T.59, W.112, H.114 Chain B: S.93, D.94, S.95, K.97 Chain O: Q.332, N.361 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.94, B:K.97, A:S.34, A:S.34, A:H.53, A:N.55, A:T.59, A:T.59 NAG-NAG-BMA-MAN-MAN-MAN.12: 15 residues within 4Å: Chain C: S.34, D.51, H.53, N.55, A.57, T.58, W.112, H.114 Chain D: D.94, S.95, K.97 Chain P: S.357, N.361 Ligands: NAG-NAG.11, NAG-NAG.11 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.34, C:S.34, C:D.51, C:N.55, D:D.94, D:K.97

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

NAG-FUC.5: 5 residues within 4Å: Chain M: Q.65 Chain O: E.57, N.58, G.505 Ligands: NAG.32 1 PLIP interactions: 1 interactions with chain O Hydrophobic interactions: O:E.57 Hydrogen bonds: O:N.58

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

NAG-NAG.6: 7 residues within 4Å: Chain D: R.53 Chain P: V.104, T.105, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:Y.135 NAG-NAG.7: 7 residues within 4Å: Chain K: D.73, Y.75 Chain O: R.278 Chain P: V.144, R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain P: Q.332, T.341, T.342, N.355, S.357, R.387 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain F: R.53 Chain Q: V.104, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:Y.135 NAG-NAG.17: 4 residues within 4Å: Chain Q: N.355, S.357, P.385 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.18 No protein-ligand interaction detected (PLIP)

2 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.8: 12 residues within 4Å: Chain P: E.34, S.179, E.181, P.182, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.40 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:G.348, P:V.414 NAG-NAG-BMA-MAN-MAN.15: 11 residues within 4Å: Chain H: Y.28, G.29, S.30, W.65, G.66, P.67, Y.69, Y.89 Chain Q: N.246, I.247, T.248 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.29, H:Y.69

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.9: 13 residues within 4Å: Chain L: Y.28, G.29, S.63, R.64, W.65, G.66, P.67, D.68, Y.69, Y.89 Chain P: N.246, I.247 Ligands: NAG.36 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-MAN.16: 23 residues within 4Å: Chain E: D.27, S.28, R.29, H.33, R.98, R.102, I.103, Y.104, G.105, V.106, V.107, F.113 Chain F: S.50, S.51, Q.52 Chain Q: N.265, T.267, D.294, R.296, H.299, N.301, T.383, R.412 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.107 Hydrogen bonds: E:V.107

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-MAN-MAN.18: 11 residues within 4Å: Chain E: A.57, T.58, T.59, W.112, H.114 Chain F: S.93, D.94, S.95 Chain Q: S.357, N.361 Ligands: NAG-NAG.17 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.114

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

NAG.19: 4 residues within 4Å: Chain O: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain O: K.202, F.203, N.204, P.208 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain O: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain O: N.103 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain B: R.53 Chain O: V.104, N.118, Y.135, L.137, D.290 Ligand excluded by PLIP NAG.24: 7 residues within 4Å: Chain I: D.73, Y.75 Chain O: V.144, R.162, N.167, T.168 Chain Q: R.278 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain O: N.308, W.364 Ligand excluded by PLIP NAG.26: 6 residues within 4Å: Chain O: Q.332, T.341, T.342, N.355, S.357, R.387 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain O: S.261, N.416 Ligands: NAG-NAG-BMA-MAN.2 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain O: Q.263, N.265, R.412, V.414 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain O: D.200, Q.210, N.211 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain O: E.238, E.239, V.240, N.259, T.260, K.313 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain O: N.589, S.591 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain M: F.57 Chain O: N.603 Ligands: NAG-FUC.5 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain O: K.611, E.612, N.615 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain P: N.103, D.111, M.112 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain P: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain P: K.202, N.204, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.9 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain P: Q.263, N.265, V.414 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain P: N.271, I.292, Q.408, V.410 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain P: N.308, W.364 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain P: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.8 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain P: E.57, N.58, S.506 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain P: D.200, K.201, N.211 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain P: E.238, E.239, N.259, T.260, K.313 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain P: N.589, L.623 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain Q: C.101, T.102, N.103 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain Q: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.47: 6 residues within 4Å: Chain G: Y.75 Chain P: R.278 Chain Q: V.144, R.162, N.167, T.168 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain Q: N.204, T.206, S.244 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain Q: Q.263, N.265, R.412, V.414 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain Q: N.271, I.292, V.410 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain Q: S.261, N.416 Ligands: NAG-NAG-BMA.14 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain Q: E.57, N.58, S.506 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain Q: N.211 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain Q: E.238, N.259, T.260, K.313 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain Q: N.308, W.364 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain Q: N.589, S.590 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain Q: K.611, E.612, N.615 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rantalainen, K. et al., Virus glycoprotein nanodisc platform for vaccine design. Biorxiv (2025)

Release Date

2025-07-30

Peptides

BG18 Fab heavy chain: ACE
BG18 Fab light chain: BDF
VRC01 Fab heavy chain: GIK
VRC01 Fab light chain: HJL
3BC315 Fab heavy chain: M
3BC315 Fab light chain: N
Envelope glycoprotein gp160: OPQ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
F

E
I

B
E

D
G

F
J

G
K

I
N

K
P

H
M

J
O

L
Q

M
H

N
L

O
A

P
B

Q
C

BG18 Fab heavy chain

BG18 Fab light chain

VRC01 Fab heavy chain

VRC01 Fab light chain

3BC315 Fab heavy chain

3BC315 Fab light chain

Envelope glycoprotein gp160

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