SMTL ID : 7ly9.1

Cryo-EM structure of 2909 Fab in complex with 3BNC117 Fab and CAP256.wk34.c80 SOSIP.RnS2 N160K HIV-1 Env trimer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

7 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: 5 residues within 4Å: Chain C: E.233, I.234, N.253, E.254, R.307 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.295, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain G: E.232, E.233, I.234, N.253, E.254, R.307 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain G: T.261, H.293, N.295, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 11 residues within 4Å: Chain K: D.175, P.176, K.216, V.218, L.225, N.226, N.338, C.403, K.404, S.405 Ligands: NAG.59 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:K.404 Hydrogen bonds: K:D.175 NAG-NAG.10: 6 residues within 4Å: Chain K: E.232, E.233, I.234, N.253, R.307, E.310 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:E.310 NAG-NAG.11: 4 residues within 4Å: Chain K: H.293, N.295, T.371, T.373 No protein-ligand interaction detected (PLIP)

3 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.3: 9 residues within 4Å: Chain C: E.239, N.240 Chain E: G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.28 Hydrogen bonds: E:R.62, E:R.62 NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 8 residues within 4Å: Chain G: E.239, N.240 Chain I: G.27, Y.28, R.62, W.63, G.64 Ligands: NAG.42 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.62, I:R.62 NAG-NAG-BMA-MAN-MAN-MAN-MAN.12: 8 residues within 4Å: Chain K: E.239, N.240 Chain M: G.27, Y.28, R.62, W.63, G.64 Ligands: NAG.53 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:Y.28 Hydrogen bonds: M:G.27, M:R.62, M:R.62

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.4: 8 residues within 4Å: Chain C: T.173, D.175, N.226, N.338, T.402, C.403, K.404, S.405 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.175, C:K.404

1 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 G: D.175, P.176, L.225, N.226, K.404, S.405 Ligands: NAG.38 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain C: N.194, T.196, N.204 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain C: N.193, N.205 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain C: N.265, I.286, G.399, N.400 Ligands: NAG.19 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain C: N.317 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain C: I.321, N.323, T.425, R.427 Ligands: NAG.22 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: N.347, S.349 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain C: P.263, N.265, R.290, N.400 Ligands: NAG.15 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: L.229, S.255, K.404, N.406 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: W.3, N.460 Chain F: N.97 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.354 Ligands: NAG.17 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: N.161, T.162 Chain D: S.75, W.76 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.93 Chain C: N.98, E.154 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain C: K.103, N.117, L.136, G.283, D.284 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: N.198, T.200, S.238, L.241 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: E.55, N.56 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: T.20, T.22, N.68 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain F: N.101, S.103 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain F: R.123, N.127 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: R.53 Chain G: N.98, E.154 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain G: K.103, N.117, R.132, Y.134, D.284 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain G: N.194, N.204 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain G: N.205 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain G: N.265, G.399, N.400 Ligands: NAG.37 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: I.321, N.323, K.423 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: P.263, N.400 Ligands: NAG.35 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain G: K.216, S.255, N.406 Ligands: NAG-NAG-BMA.8 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.354, T.356 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: R.156, N.161, T.162 Chain H: W.76 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain G: E.55, N.56 Chain J: S.18 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain G: N.198, T.200, I.236, H.315 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain G: W.3, E.458, C.459, N.460 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: N.419, S.421 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: R.313, N.317 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.347 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain I: T.20, T.22, E.66, N.68 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain J: E.124, N.127 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain J: N.101, S.103, W.104 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain B: N.54 Chain K: N.98 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain K: K.103, N.117, S.119, Y.134 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain K: N.194, K.195, N.204 Ligand excluded by PLIP NAG.53: 6 residues within 4Å: Chain K: N.198, G.199, T.200, S.238, L.241 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.12 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain K: N.193, N.205 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain K: N.265, I.286, G.399, N.400 Ligands: NAG.58 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain K: N.323 Chain L: R.62 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain K: T.334, N.347 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain K: N.400, T.402 Ligands: NAG.55 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain K: K.216, N.226, S.255, N.406 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain K: N.354, T.356 Ligand excluded by PLIP NAG.61: 7 residues within 4Å: Chain K: R.156, N.161, T.162 Chain L: H.73, A.74, S.75, W.76 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain K: W.3, N.460 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain K: E.55, N.56 Chain N: S.18 Ligand excluded by PLIP NAG.64: 5 residues within 4Å: Chain M: T.22, R.61, W.63, E.66, N.68 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain N: N.101, S.103 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain N: N.127, Y.128 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, M. et al., Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces. Nat Commun (2021)

Release Date

2021-08-18

Peptides

2909 Light Chain: A
2909 Heavy Chain: B
Envelope glycoprotein gp120: CGK
3BNC117 Heavy Chain: DHL
3BNC117 Light Chain: EIM
Envelope glycoprotein gp41: FJN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
G

G
D

K
K

D
B

H
E

L
A

E
C

I
I

M
M

F
F

J
J

N
N

2909 Light Chain

2909 Heavy Chain

Envelope glycoprotein gp120

3BNC117 Heavy Chain

3BNC117 Light Chain

Envelope glycoprotein gp41

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