SMTL ID : 6ozc.1

BG505 SOSIP.664 with 2G12 Fab2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-6-6-mer

Ligands

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.1: 12 residues within 4Å: Chain A: S.179, E.181, P.182, K.222, L.231, N.232, N.346, G.348, G.409, V.414, S.415 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.11: 12 residues within 4Å: Chain G: S.179, E.181, P.182, K.222, L.231, N.232, N.346, G.348, G.409, V.414, S.415 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.21: 12 residues within 4Å: Chain M: S.179, E.181, P.182, K.222, L.231, N.232, N.346, G.348, G.409, V.414, S.415 Ligands: NAG-NAG.28 No protein-ligand interaction detected (PLIP)

6 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.2: 6 residues within 4Å: Chain A: N.332, S.333, T.341 Ligands: NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 7 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.12: 6 residues within 4Å: Chain G: N.332, S.333, T.341 Ligands: NAG-NAG-BMA-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 7 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 6 residues within 4Å: Chain M: N.332, S.333, T.341 Ligands: NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.24: 7 residues within 4Å: Chain M: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.22, NAG-NAG-BMA-MAN-MAN.22, NAG-NAG-BMA-MAN-MAN.22, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.23, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.23 No protein-ligand interaction detected (PLIP)

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.3: 20 residues within 4Å: Chain A: S.357, N.361 Chain C: W.32, G.93, Y.94 Chain D: A.31, H.32, T.33, T.53, T.56, Y.57, K.99, G.100, S.105, D.106, N.107, D.108 Ligands: NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.106 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13: 20 residues within 4Å: Chain G: S.357, N.361 Chain I: W.32, G.93, Y.94 Chain J: A.31, H.32, T.33, T.53, T.56, Y.57, K.99, G.100, S.105, D.106, N.107, D.108 Ligands: NAG-NAG-BMA-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN.14 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:D.106 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.23: 20 residues within 4Å: Chain M: S.357, N.361 Chain O: W.32, G.93, Y.94 Chain P: A.31, H.32, T.33, T.53, T.56, Y.57, K.99, G.100, S.105, D.106, N.107, D.108 Ligands: NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:D.106

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.5: 12 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, T.383 Chain D: F.27, R.28, L.75, E.76, D.77 Chain F: S.55, R.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.15: 12 residues within 4Å: Chain G: N.265, T.267, H.299, N.301, T.383 Chain J: F.27, R.28, L.75, E.76, D.77 Chain L: S.55, R.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.25: 12 residues within 4Å: Chain M: N.265, T.267, H.299, N.301, T.383 Chain P: F.27, R.28, L.75, E.76, D.77 Chain R: S.55, R.58 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: 20 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412, V.414 Chain E: G.93, Y.94 Chain F: A.31, H.32, T.33, T.53, T.56, K.99, G.100, L.104, S.105, D.106, N.107, D.108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.16: 20 residues within 4Å: Chain G: Q.263, N.265, N.301, S.303, R.412, V.414 Chain K: G.93, Y.94 Chain L: A.31, H.32, T.33, T.53, T.56, K.99, G.100, L.104, S.105, D.106, N.107, D.108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.26: 20 residues within 4Å: Chain M: Q.263, N.265, N.301, S.303, R.412, V.414 Chain Q: G.93, Y.94 Chain R: A.31, H.32, T.33, T.53, T.56, K.99, G.100, L.104, S.105, D.106, N.107, D.108 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- 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-(1-2)-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-MAN-MAN-MAN.7: 11 residues within 4Å: Chain A: K.304, A.305, N.308, S.362, W.364 Chain D: S.55, R.58 Chain F: R.28, L.75, E.76, D.77 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.17: 11 residues within 4Å: Chain G: K.304, A.305, N.308, S.362, W.364 Chain J: S.55, R.58 Chain L: R.28, L.75, E.76, D.77 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.27: 11 residues within 4Å: Chain M: K.304, A.305, N.308, S.362, W.364 Chain P: S.55, R.58 Chain R: R.28, L.75, E.76, D.77 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.8: 5 residues within 4Å: Chain A: N.232, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: V.104, N.106, N.118, Y.135, L.137 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.135 Hydrogen bonds: A:Y.135 NAG-NAG.18: 5 residues within 4Å: Chain G: N.232, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain G: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain G: V.104, N.106, N.118, Y.135, L.137 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Y.135 Hydrogen bonds: G:Y.135 NAG-NAG.28: 5 residues within 4Å: Chain M: N.232, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain M: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain M: V.104, N.106, N.118, Y.135, L.137 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:Y.135 Hydrogen bonds: M:Y.135

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

NAG.31: 2 residues within 4Å: Chain A: T.102, N.103 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.204, T.206, S.244 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: R.162, N.167, T.168 Chain M: R.278 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.100, S.101 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.105, R.106, N.107 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain G: T.102, N.103 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain G: N.204, T.206, S.244 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: R.278 Chain G: R.162, N.167, T.168 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain H: N.100, S.101 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain H: N.105, R.106, N.107 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain H: E.123, N.126 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain M: T.102, N.103 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain M: N.204, T.206, S.244 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain M: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain G: R.278 Chain M: R.162, N.167, T.168 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain N: N.100, S.101 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain N: N.105, R.106, N.107 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain N: E.123, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seabright, G.E. et al., Networks of HIV-1 Envelope Glycans Maintain Antibody Epitopes in the Face of Glycan Additions and Deletions. Structure (2020)

Release Date

2020-05-20

Peptides

Envelope glycoprotein gp160: AGM
Envelope glycoprotein gp41: BHN
2G12 Fab light chain: CEIKOQ
2G12 Fab Heavy chain: DFJLPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
E

M
F

B
B

H
G

N
I

C
L

E
D

I
Q

K
M

O
R

Q
N

D
H

F
C

J
O

L
J

P
P

R
K

Envelope glycoprotein gp160

Envelope glycoprotein gp41

2G12 Fab light chain

2G12 Fab Heavy chain

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