SMTL ID : 6udj.1

HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074

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- 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.1: 19 residues within 4Å: Chain C: R.103, I.104, Y.105, G.106, V.107, V.108 Chain G: S.25, N.45, N.46, Q.47, P.61, D.62, I.63 Chain N: N.263, T.265, R.294, H.297, N.299, T.381 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain C Hydrogen bonds: N:R.294, N:R.294, C:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2: 20 residues within 4Å: Chain B: R.103, I.104, Y.105, G.106, V.107, V.108 Chain I: S.25, N.45, N.46, Q.47, P.61, D.62, I.63 Chain P: N.263, T.265, R.294, H.297, N.299, T.381 Ligands: NAG-NAG.25 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain P Hydrogen bonds: B:V.108, P:R.294, P:R.294 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.3: 20 residues within 4Å: Chain A: R.103, I.104, Y.105, G.106, V.107, V.108 Chain K: S.25, N.45, N.46, Q.47, P.61, D.62, I.63 Chain R: N.263, T.265, R.294, H.297, N.299, S.379, T.381 3 PLIP interactions: 2 interactions with chain R, 1 interactions with chain A Hydrogen bonds: R:R.294, R:R.294, A:V.108

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

NAG-NAG.4: 5 residues within 4Å: Chain M: L.9, G.16, S.17 Chain N: E.55, N.56 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain N: N.101, G.112 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain N: Q.98, S.118, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain N: N.202, T.204, S.242, E.243 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain N: Q.261, N.263, V.300, S.301, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain N: S.355, G.356, N.359 Ligands: NAG-NAG-BMA.13, NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain O: G.16, S.17 Chain P: E.55, N.56 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain P: N.101 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain P: Q.98, S.118, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain P: N.202, T.204, S.242, E.243 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 7 residues within 4Å: Chain P: Q.261, N.263, N.299, V.300, S.301, V.412 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain P: S.355, G.356, N.359 Ligands: NAG-NAG-BMA.27, NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain Q: G.16, S.17 Chain R: E.55, N.56 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 1 residues within 4Å: Chain R: N.101 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain R: Q.98, S.118, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 5 residues within 4Å: Chain R: N.202, T.204, S.242, E.243 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.38 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 6 residues within 4Å: Chain R: Q.261, N.263, N.299, V.300, S.301, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 5 residues within 4Å: Chain R: S.355, G.356, N.359 Ligands: NAG-NAG-BMA.41, NAG-NAG-BMA.41 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.6: 4 residues within 4Å: Chain G: R.92 Chain N: N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 12 residues within 4Å: Chain N: K.33, E.179, P.180, V.222, L.229, N.230, N.344, C.345, C.411, V.412, S.413 Ligands: NAG-NAG-BMA.16 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:E.179, N:V.412 NAG-NAG-BMA-MAN-MAN.20: 4 residues within 4Å: Chain I: R.92 Chain P: N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.31: 12 residues within 4Å: Chain P: K.33, E.179, P.180, V.222, L.229, N.230, N.344, G.346, C.411, V.412, S.413 Ligands: NAG-NAG-BMA.30 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:G.346, P:V.412 NAG-NAG-BMA-MAN-MAN.34: 6 residues within 4Å: Chain K: R.92 Chain R: V.102, N.116, Y.133, L.135, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.45: 11 residues within 4Å: Chain R: K.33, E.179, P.180, V.222, L.229, N.230, N.344, G.346, V.412, S.413 Ligands: NAG-NAG-BMA.44 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:G.346, R:V.412

6 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.8: 6 residues within 4Å: Chain J: R.38, P.47 Chain N: R.160, N.165, T.166 Chain P: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 3 residues within 4Å: Chain N: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.22: 6 residues within 4Å: Chain L: R.38, P.47 Chain P: R.160, N.165, T.166 Chain R: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 3 residues within 4Å: Chain P: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.36: 7 residues within 4Å: Chain H: R.38, P.47 Chain N: R.276 Chain R: V.142, R.160, N.165, T.166 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.40: 3 residues within 4Å: Chain R: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.10: 13 residues within 4Å: Chain E: R.43, Q.46, G.47, L.48, D.49, S.50, S.87, G.88, A.89, D.90 Chain N: N.244, T.246 Ligands: NAG-NAG.9 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.88, E:S.50, E:S.50, E:S.87, E:G.47, E:G.47 NAG-NAG-BMA-MAN-MAN-MAN.24: 11 residues within 4Å: Chain F: R.43, G.47, L.48, D.49, S.87, G.88, A.89, D.90 Chain P: N.244, T.246 Ligands: NAG-NAG.23 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.88, F:S.87, F:G.47, F:G.47 NAG-NAG-BMA-MAN-MAN-MAN.38: 12 residues within 4Å: Chain D: R.43, Q.46, G.47, L.48, D.49, S.87, G.88, A.89, D.90 Chain R: N.244, T.246 Ligands: NAG-NAG.37 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.88, D:G.47, D:G.47 Hydrophobic interactions: D:Q.46

9 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.13: 6 residues within 4Å: Chain N: N.353, S.355 Ligands: NAG-NAG.14, NAG-NAG-BMA.15, NAG-NAG-BMA.15, NAG-NAG-BMA.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain N: N.330, T.339, N.353, S.355 Ligands: NAG-NAG-BMA.13, NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 5 residues within 4Å: Chain N: N.230, L.233, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 6 residues within 4Å: Chain P: N.353, S.355 Ligands: NAG-NAG.28, NAG-NAG-BMA.29, NAG-NAG-BMA.29, NAG-NAG-BMA.29 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 6 residues within 4Å: Chain P: N.330, T.339, N.353, S.355 Ligands: NAG-NAG-BMA.27, NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 5 residues within 4Å: Chain P: N.230, L.233, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 5 residues within 4Å: Chain R: N.353, S.355 Ligands: NAG-NAG.42, NAG-NAG-BMA.43, NAG-NAG-BMA.43 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 6 residues within 4Å: Chain R: N.330, T.339, N.353, S.355 Ligands: NAG-NAG-BMA.41, NAG-NAG-BMA.41 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.44: 5 residues within 4Å: Chain R: N.230, L.233, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.45 No protein-ligand interaction detected (PLIP)

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

NAG.46: 2 residues within 4Å: Chain M: N.100, S.102 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain M: N.126 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain M: N.107, S.109, E.110 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain N: N.306, W.362 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain N: N.322 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain O: N.100, S.102 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain O: N.126 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain O: N.107, S.109, E.110 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain P: N.306, W.362 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain P: N.322 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain Q: N.100, S.102 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain Q: N.126 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain Q: N.107, E.110 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain R: N.306, W.362 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain R: N.322 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schommers, P. et al., Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. Cell (2020)

Release Date

2020-01-29

Peptides

10-1074 Fab Heavy Chain: ABC
1-18 Fab Light Chain: DEF
10-1074 Fab Light Chain: GIK
1-18 Fab Heavy Chain: HJL
Envelope glycoprotein gp41: MOQ
Envelope glycoprotein gp120: NPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
K

C
Q

D
E

E
O

F
I

G
B

I
L

K
R

H
D

J
N

L
H

M
C

O
M

Q
F

N
G

P
J

R
P

10-1074 Fab Heavy Chain

1-18 Fab Light Chain

10-1074 Fab Light Chain

1-18 Fab Heavy Chain

Envelope glycoprotein gp41

Envelope glycoprotein gp120

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