SMTL ID : 9bio.1

Structure of VRC44.01 Fab in complex with 3BNC117-purified C1080.c3 RnS SOSIP.664 HIV-1 Env trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- FUC: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-FUC.1: 13 residues within 4Å: Chain A: Q.110, N.114 Chain E: Y.56 Chain F: Q.1, S.2, R.26, Y.27, F.32, R.98, H.100, T.101, D.109, F.110 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Q.1, F:Y.27 Hydrogen bonds: F:Q.1, F:Q.1, F:S.2, F:R.98, F:R.98 NAG-NAG-BMA-MAN-MAN-MAN-FUC.15: 14 residues within 4Å: Chain G: Q.110, N.114, E.119 Chain K: Y.56 Chain L: Q.1, Y.3, R.26, Y.27, F.32, R.98, H.100, T.101, D.109, F.110 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:Y.27 Hydrogen bonds: L:Q.1, L:R.98, L:R.98 NAG-NAG-BMA-MAN-MAN-MAN-FUC.29: 15 residues within 4Å: Chain M: Q.110, N.114, E.119 Chain Q: Y.56, G.57 Chain R: Q.1, S.2, R.26, Y.27, F.32, R.98, H.100, T.101, D.109, F.110 6 PLIP interactions: 6 interactions with chain R Hydrogen bonds: R:Q.1, R:Q.1, R:S.2, R:R.98, R:R.98 Hydrophobic interactions: R:Q.1, R:Y.27

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

NAG-NAG.2: 5 residues within 4Å: Chain B: V.104, T.105, L.106, N.127, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: T.98, S.100, S.129, N.131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: N.114, N.265, Y.299, E.301, K.405, V.409 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.405 NAG-NAG.9: 4 residues within 4Å: Chain B: N.232, S.261, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.303, T.305, K.306, D.374 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: Y.55, N.199, K.201, N.211 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.201, B:K.201 NAG-NAG.13: 5 residues within 4Å: Chain B: G.238, E.239, I.240, N.259, K.317 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain G: E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain H: V.104, T.105, L.106, N.127, Y.144, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain H: T.98, S.100, S.129, N.131 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain H: N.114, N.265, Y.299, E.301, K.405, V.409 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:K.405 NAG-NAG.23: 4 residues within 4Å: Chain H: N.232, S.261, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain H: N.303, T.305, K.306, D.374 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain H: Y.55, N.199, K.201, N.211 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:K.201, H:K.201 NAG-NAG.27: 5 residues within 4Å: Chain H: G.238, E.239, I.240, N.259, K.317 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain M: E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain N: V.104, T.105, L.106, N.127, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain N: T.98, S.100, S.129, N.131 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain N: N.114, N.265, Y.299, E.301, V.409 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 4 residues within 4Å: Chain N: N.232, S.261, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain N: N.303, T.305, K.306, D.374 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 4 residues within 4Å: Chain N: Y.55, N.199, K.201, N.211 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:K.201, N:K.201 NAG-NAG.41: 4 residues within 4Å: Chain N: E.239, I.240, N.259, K.317 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.4: 6 residues within 4Å: Chain B: V.153, R.162, N.167 Chain C: R.19, H.73, W.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.19 NAG-NAG-BMA-MAN-MAN.18: 5 residues within 4Å: Chain H: R.162, N.167 Chain I: R.19, H.73, W.76 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.19 NAG-NAG-BMA-MAN-MAN.32: 6 residues within 4Å: Chain N: V.153, R.162, N.167 Chain O: R.19, H.73, W.76 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:R.19

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.5: 15 residues within 4Å: Chain B: A.35, K.177, I.178, S.179, V.224, N.232, R.274, N.345, R.347, R.403, C.408, V.409, S.410 Chain I: Q.1 Ligands: NAG-NAG.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain I Hydrogen bonds: B:R.347, B:R.347, B:R.403, I:Q.1, B:V.409 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.19: 15 residues within 4Å: Chain H: A.35, K.177, I.178, S.179, V.224, N.232, R.274, N.345, R.347, R.403, C.408, V.409, S.410 Chain O: Q.1 Ligands: NAG-NAG.23 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain O Hydrogen bonds: H:R.347, H:R.347, H:R.403, O:Q.1, H:V.409 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.33: 15 residues within 4Å: Chain C: Q.1 Chain N: A.35, K.177, I.178, S.179, V.224, N.232, R.274, N.345, R.347, R.403, C.408, V.409, S.410 Ligands: NAG-NAG.37 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain C Hydrogen bonds: N:R.347, C:Q.1, N:R.347, N:R.403, N:V.409 Hydrophobic interactions: N:V.409

6 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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.6: 10 residues within 4Å: Chain B: E.245, N.246 Chain D: G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 Ligands: NAG.46 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.28 Hydrogen bonds: D:G.27, D:R.62, D:R.62 NAG-NAG-BMA-MAN-MAN-MAN-MAN.10: 20 residues within 4Å: Chain A: F.9, G.16, S.17 Chain B: E.57, N.58 Chain E: F.91, F.94, F.96 Chain F: T.30, F.31, G.33, W.50, S.52, Y.54, H.57, I.59, R.102, D.104, S.105, R.106 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.104, F:S.52, F:R.102 NAG-NAG-BMA-MAN-MAN-MAN-MAN.20: 10 residues within 4Å: Chain H: E.245, N.246 Chain J: G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 Ligands: NAG.58 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:Y.28 Hydrogen bonds: J:R.62, J:R.62 NAG-NAG-BMA-MAN-MAN-MAN-MAN.24: 21 residues within 4Å: Chain G: G.16, S.17 Chain H: E.57, N.58 Chain K: F.91, F.94, F.96 Chain L: T.30, F.31, G.33, W.50, S.52, Y.54, H.57, I.59, D.99, R.102, Q.103, D.104, S.105, R.106 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:D.104, L:S.52, L:R.102 NAG-NAG-BMA-MAN-MAN-MAN-MAN.34: 10 residues within 4Å: Chain N: E.245, N.246 Chain P: G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 Ligands: NAG.69 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:R.62, P:R.62, P:R.62 Hydrophobic interactions: P:Y.28 NAG-NAG-BMA-MAN-MAN-MAN-MAN.38: 21 residues within 4Å: Chain M: G.16, S.17 Chain N: E.57, N.58 Chain Q: F.91, F.94, F.96 Chain R: T.30, F.31, G.33, W.50, S.52, Y.54, H.57, I.59, D.99, R.102, Q.103, D.104, S.105, R.106 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:D.104, R:S.52, R:R.102

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.8: 4 residues within 4Å: Chain B: T.340, M.341, N.354, T.356 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 4 residues within 4Å: Chain H: T.340, M.341, N.354, T.356 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 4 residues within 4Å: Chain N: T.340, M.341, N.354, T.356 No protein-ligand interaction detected (PLIP)

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

NAG.42: 2 residues within 4Å: Chain A: E.123, N.126 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain A: N.105 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain A: N.100, T.102, Y.127, Q.130 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.103 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: N.204, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.6 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: N.271, T.273, I.292 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.360 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain B: N.120, T.122 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain B: P.323, N.324 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain B: N.373, D.374, T.375 Ligand excluded by PLIP NAG.52: 7 residues within 4Å: Chain B: G.304, T.305, N.308, S.361, Y.372, N.373, T.375 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain D: T.20, R.61, W.63, E.66, N.68 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain G: N.105 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain G: N.100, T.102, W.103, Y.127, Q.130 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain H: N.103 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain H: N.204, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.20 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain H: N.271, T.273, I.292 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain H: N.360 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain H: N.120, T.122 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain H: P.323, N.324 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain H: N.373, D.374, T.375 Ligand excluded by PLIP NAG.64: 5 residues within 4Å: Chain H: N.308, W.363, Y.372, N.373, T.375 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain J: R.61, E.66, N.68 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain M: N.105 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain M: N.100, T.102, Y.127, Q.130 Ligand excluded by PLIP NAG.68: 1 residues within 4Å: Chain N: N.103 Ligand excluded by PLIP NAG.69: 3 residues within 4Å: Chain N: N.204, T.206 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.34 Ligand excluded by PLIP NAG.70: 3 residues within 4Å: Chain N: N.271, T.273, I.292 Ligand excluded by PLIP NAG.71: 1 residues within 4Å: Chain N: N.360 Ligand excluded by PLIP NAG.72: 2 residues within 4Å: Chain N: N.120, T.122 Ligand excluded by PLIP NAG.73: 2 residues within 4Å: Chain N: P.323, N.324 Ligand excluded by PLIP NAG.74: 3 residues within 4Å: Chain N: N.373, D.374, T.375 Ligand excluded by PLIP NAG.75: 3 residues within 4Å: Chain N: N.308, W.363, T.375 Ligand excluded by PLIP NAG.76: 5 residues within 4Å: Chain P: T.20, R.61, W.63, E.66, N.68 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.56: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cale, E.M. et al., A multidonor class of highly glycan-dependent HIV-1 gp120-gp41 interface-targeting broadly neutralizing antibodies. Cell Rep (2024)

Release Date

2024-11-13

Peptides

Envelope glycoprotein gp41: AGM
Envelope glycoprotein gp160: BHN
3BNC117 heavy chain: CIO
3BNC117 light chain: DJP
VRC44.01 light chain: EKQ
VRC44.01 heavy chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

G
A

M
J

B
G

H
C

N
K

C
S

I
D

O
M

D
U

J
E

P
N

E
L

K
F

Q
O

F
H

L
I

R
P

Envelope glycoprotein gp41

Envelope glycoprotein gp160

3BNC117 heavy chain

3BNC117 light chain

VRC44.01 light chain

VRC44.01 heavy chain

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