SMTL ID : 7t4g.1

The Envelope Glycoprotein SIVmac239.K180S SOSIP trimer in complex with 3 copies of the neutralizing antibody K11

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 18 residues within 4Å: Chain A: N.37, S.74, F.75, D.76, N.79, F.251, M.252, P.253, G.292, R.293, K.498 Chain C: N.125, F.126, Y.128 Chain D: N.49, N.71, G.85, S.86 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.251 Hydrogen bonds: A:S.74, A:R.293 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.14: 20 residues within 4Å: Chain E: N.37, S.74, F.75, D.76, N.79, F.251, M.252, P.253, G.292, R.293, K.498 Chain G: N.125, F.126, Y.128 Chain H: N.49, S.50, N.71, G.85, S.86 Ligands: NAG-NAG-BMA.21 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.293, E:S.74, E:R.293 Hydrophobic interactions: E:F.251 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27: 21 residues within 4Å: Chain I: N.37, S.74, F.75, D.76, N.79, F.251, M.252, P.253, G.292, R.293, K.498 Chain K: N.125, F.126, Y.128 Chain L: N.49, S.50, N.71, G.85, S.86 Ligands: NAG-NAG-BMA-MAN.34, NAG.65 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.293, I:S.74 Hydrophobic interactions: I:F.251

11 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: 3 residues within 4Å: Chain A: N.114, E.117, R.338 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.316 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 8 residues within 4Å: Chain A: I.152, A.153, R.312, W.345, R.396, T.458, N.460 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.152, A:A.153 Hydrogen bonds: A:R.312 NAG-NAG.13: 4 residues within 4Å: Chain A: D.471, W.472, Q.477, N.479 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain E: N.114, S.116 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain E: N.316, D.456 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 7 residues within 4Å: Chain E: I.152, A.153, R.312, W.345, T.458, N.460 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.19 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.152, E:A.153 Hydrogen bonds: E:R.312, E:R.312 NAG-NAG.26: 2 residues within 4Å: Chain E: D.471, N.479 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain I: N.114, S.116, R.338 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain I: N.316, G.455, D.456 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 8 residues within 4Å: Chain I: I.152, A.153, R.312, W.345, R.396, T.458, N.460 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.32 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:I.152, I:A.153 Hydrogen bonds: I:R.312

12 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 3 residues within 4Å: Chain A: M.144, N.146, T.148 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.4: 2 residues within 4Å: Chain A: Q.154, N.156 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.5: 7 residues within 4Å: Chain A: V.193, C.194, E.195, Q.196, N.212, T.213 Chain E: K.176 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:K.176, E:K.176, A:Q.196 NAG-NAG-FUC.10: 1 residues within 4Å: Chain A: N.371 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.16: 3 residues within 4Å: Chain E: M.144, N.146, T.148 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.17: 4 residues within 4Å: Chain E: Q.154, N.156, C.157, T.158 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.18: 6 residues within 4Å: Chain E: V.193, C.194, E.195, N.212, T.213 Chain I: K.176 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain I Hydrogen bonds: E:Q.196, I:K.176, I:K.176 NAG-NAG-FUC.23: 3 residues within 4Å: Chain E: N.371, N.372 Chain G: G.44 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:N.371 NAG-NAG-FUC.29: 3 residues within 4Å: Chain I: M.144, N.146, T.148 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.30: 4 residues within 4Å: Chain I: Q.154, N.156, C.157, T.158 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.31: 6 residues within 4Å: Chain A: K.176 Chain I: V.193, C.194, E.195, N.212, T.213 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A Hydrogen bonds: I:Q.196, A:K.176 NAG-NAG-FUC.36: 3 residues within 4Å: Chain I: N.371, N.372 Chain K: G.44 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.6: 12 residues within 4Å: Chain A: K.222, W.225, D.226, N.278, N.394, R.396, R.453, E.454, C.459, N.460, S.461 Ligands: NAG-NAG.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.460 Hydrogen bonds: A:W.225, A:N.460 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 13 residues within 4Å: Chain E: K.222, W.225, D.226, Q.270, N.278, N.394, R.396, R.453, E.454, C.459, N.460, S.461 Ligands: NAG-NAG.25 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:N.460 Hydrogen bonds: E:W.225, E:N.460 NAG-NAG-BMA-MAN-MAN-MAN-MAN.32: 12 residues within 4Å: Chain I: D.50, K.222, W.225, D.226, Q.270, N.278, N.394, R.453, C.459, N.460, S.461 Ligands: NAG-NAG.38 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:N.460 Hydrogen bonds: I:W.225, I:N.460

2 x NAG- NAG- BMA- MAN: 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.7: 5 residues within 4Å: Chain A: N.284, N.302, Y.304, Y.305, E.356 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.304, A:Y.305 Hydrogen bonds: A:Y.304 NAG-NAG-BMA-MAN.33: 5 residues within 4Å: Chain I: N.284, N.302, Y.304, Y.305, E.356 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:Y.304, I:Y.305 Hydrogen bonds: I:Y.304

5 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: 7 residues within 4Å: Chain A: R.293, D.294, N.295, T.368, W.472, I.473 Chain C: N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.368 NAG-NAG-BMA.11: 8 residues within 4Å: Chain A: K.358, T.373, D.374, I.376, N.377, E.412, D.413, R.414 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.412, A:D.413, A:D.413 NAG-NAG-BMA.21: 9 residues within 4Å: Chain E: G.292, R.293, D.294, N.295, R.366, T.368, W.472 Chain G: N.125 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.14 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.368 NAG-NAG-BMA.24: 8 residues within 4Å: Chain E: K.358, T.373, D.374, I.376, N.377, E.412, D.413, R.414 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:D.413 Hydrogen bonds: E:E.412, E:D.413, E:D.413 NAG-NAG-BMA.39: 3 residues within 4Å: Chain I: D.471, Q.477, N.479 No protein-ligand interaction detected (PLIP)

1 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.20: 6 residues within 4Å: Chain E: N.284, N.302, Y.304, Y.305, E.356 Chain G: M.94 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:Y.304, E:Y.305 Hydrogen bonds: E:Y.304

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.34: 9 residues within 4Å: Chain I: G.292, R.293, D.294, N.295, R.366, T.368, W.472, I.473 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:T.368 NAG-NAG-BMA-MAN.37: 8 residues within 4Å: Chain I: K.358, T.373, I.376, N.377, E.412, D.413, R.414, N.415 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:E.412, I:D.413, I:D.413

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

NAG.40: 2 residues within 4Å: Chain A: N.70 Chain B: G.15 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: N.79, R.293 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain A: R.112, N.171, S.180, K.181 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain A: E.182, Y.183, N.184, N.336 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: G.197, N.198 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: G.201, N.202 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain A: E.66, M.67, A.68, N.244, V.259 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain A: Y.304, N.306, K.349 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain A: D.474, N.476, Q.477 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain B: P.99, N.100, S.102, L.122 Ligands: NAG.51 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain B: K.106, W.107, N.108, N.109 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain B: F.121, L.122, N.125 Ligands: NAG.49 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain E: N.70 Chain F: G.15, S.16 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain E: N.79 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: R.112, N.171, S.180 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: E.182, Y.183, N.184 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain E: G.197, N.198 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain E: G.201, N.202 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain E: E.66, M.67, A.68, N.244, V.259 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain E: Y.304, N.306, K.349 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain E: D.474, N.476, Q.477 Ligand excluded by PLIP NAG.61: 7 residues within 4Å: Chain F: P.99, N.100, S.102, L.103, F.121, L.122 Ligands: NAG.63 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain F: K.106, W.107, N.108, N.109 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain F: F.121, L.122, N.125 Ligands: NAG.61 Ligand excluded by PLIP NAG.64: 5 residues within 4Å: Chain I: N.70 Chain J: T.13, A.14, G.15, S.16 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain I: N.79 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain I: R.112, N.171, S.180, K.181 Ligand excluded by PLIP NAG.67: 3 residues within 4Å: Chain I: E.182, Y.183, N.184 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain I: G.197, N.198 Ligand excluded by PLIP NAG.69: 2 residues within 4Å: Chain I: G.201, N.202 Ligand excluded by PLIP NAG.70: 5 residues within 4Å: Chain I: E.66, M.67, A.68, N.244, V.259 Ligand excluded by PLIP NAG.71: 2 residues within 4Å: Chain I: Y.304, N.306 Ligand excluded by PLIP NAG.72: 3 residues within 4Å: Chain I: I.473, D.474, N.476 Ligand excluded by PLIP NAG.73: 7 residues within 4Å: Chain J: P.99, N.100, S.102, L.103, F.121, L.122 Ligands: NAG.75 Ligand excluded by PLIP NAG.74: 2 residues within 4Å: Chain J: K.106, N.109 Ligand excluded by PLIP NAG.75: 3 residues within 4Å: Chain J: F.121, N.125 Ligands: NAG.73 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, F. et al., Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus. Nat Commun (2022)

Release Date

2022-10-19

Peptides

Envelope glycoprotein gp120: AEI
Envelope glycoprotein gp41: BFJ
K11 IgG heavy chain: CGK
K11 IgG light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
E

B
B

F
D

J
F

C
H

G
G

K
J

D
L

H
I

L
K

Envelope glycoprotein gp120

Envelope glycoprotein gp41

K11 IgG heavy chain

K11 IgG light chain

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