SMTL ID : 6nnj.1

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.1 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

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

Ligands

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.1: 21 residues within 4Å: Chain A: G.16, S.17 Chain B: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain C: H.96, N.97 Chain D: E.57, N.58 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.111, B:D.111, B:T.115, C:H.96, B:D.111, B:S.113, B:H.33, B:S.52, B:S.52, B:D.111, B:T.115 Hydrophobic interactions: B:T.115 NAG-NAG-BMA-MAN-MAN-MAN.17: 21 residues within 4Å: Chain I: G.16, S.17 Chain J: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain K: H.96, N.97 Chain L: E.57, N.58 7 PLIP interactions: 6 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:D.111, J:D.111, J:T.115, K:H.96, J:D.111, J:S.113, J:H.33, J:S.52, J:S.52, J:D.111, J:T.115 Hydrophobic interactions: J:T.115 NAG-NAG-BMA-MAN-MAN-MAN.33: 21 residues within 4Å: Chain Q: G.16, S.17 Chain R: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain S: H.96, N.97 Chain T: E.57, N.58 7 PLIP interactions: 6 interactions with chain R, 1 interactions with chain S Hydrogen bonds: R:D.111, R:D.111, R:T.115, S:H.96, R:D.111, R:S.113, R:H.33, R:S.52, R:S.52, R:D.111, R:T.115 Hydrophobic interactions: R:T.115

15 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 D: C.101, T.102, N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain D: N.246, T.248 Chain H: I.29, G.30, D.32, F.67, Y.91 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.30 NAG-NAG.6: 6 residues within 4Å: Chain D: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: N.271, T.273, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain D: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain L: C.101, T.102, N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain L: N.246, T.248 Chain P: I.29, G.30, D.32, F.67, Y.91 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.30 NAG-NAG.22: 6 residues within 4Å: Chain L: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain L: N.271, T.273, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain L: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.20 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain T: C.101, T.102, N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 7 residues within 4Å: Chain T: N.246, T.248 Chain X: I.29, G.30, D.32, F.67, Y.91 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:G.30 NAG-NAG.38: 6 residues within 4Å: Chain T: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain T: N.271, T.273, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 5 residues within 4Å: Chain T: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.36 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.3: 4 residues within 4Å: Chain D: V.104, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 4 residues within 4Å: Chain L: V.104, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.35: 4 residues within 4Å: Chain T: V.104, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP)

3 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.4: 9 residues within 4Å: Chain D: P.182, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.348 NAG-NAG-BMA-MAN.20: 9 residues within 4Å: Chain L: P.182, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.25 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.348 NAG-NAG-BMA-MAN.36: 9 residues within 4Å: Chain T: P.182, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.41 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:G.348

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.8: 22 residues within 4Å: Chain D: T.267, R.296, H.299, N.301, T.383, R.412 Chain E: Q.100, K.102, R.103, I.104, Y.105, G.106, M.107, V.108, S.109 Chain F: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:V.108, E:S.109, D:R.296, D:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.24: 22 residues within 4Å: Chain L: T.267, R.296, H.299, N.301, T.383, R.412 Chain M: Q.100, K.102, R.103, I.104, Y.105, G.106, M.107, V.108, S.109 Chain N: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 4 PLIP interactions: 2 interactions with chain M, 2 interactions with chain L Hydrogen bonds: M:V.108, M:S.109, L:R.296, L:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.40: 22 residues within 4Å: Chain T: T.267, R.296, H.299, N.301, T.383, R.412 Chain U: Q.100, K.102, R.103, I.104, Y.105, G.106, M.107, V.108, S.109 Chain V: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 4 PLIP interactions: 2 interactions with chain T, 2 interactions with chain U Hydrogen bonds: T:R.296, T:R.296, U:V.108, U:S.109

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

NAG.10: 1 residues within 4Å: Chain A: N.100 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: E.123, N.126 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain D: V.144, R.162, N.167 Chain G: R.83 Chain T: R.278 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: N.204, S.244 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain D: N.332, N.355, S.357 Ligands: NAG.16 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG.15 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain I: N.100 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain I: E.123, N.126 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain L: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain D: R.278 Chain L: V.144, R.162, N.167 Chain O: R.83 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain L: N.204, S.244 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain L: N.332, N.355, S.357 Ligands: NAG.32 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain L: N.355, S.357 Ligands: NAG.31 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain Q: N.100 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain Q: E.123, N.126 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain T: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain L: R.278 Chain T: V.144, R.162, N.167 Chain W: R.83 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain T: N.204, S.244 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain T: N.332, N.355, S.357 Ligands: NAG.48 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain T: N.355, S.357 Ligands: NAG.47 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Q. et al., Improvement of antibody functionality by structure-guided paratope engraftment. Nat Commun (2019)

Release Date

2019-02-27

Peptides

Envelope glycoprotein gp41: AIQ
35O22 scFv heavy chain: BJR
35O22 scFv light chain: CKS
Envelope glycoprotein gp120: DLT
3H109L Fab heavy chain: EMU
3H109L Fab light chain: FNV
CH31 scFv heavy chain: GOW
CH31 scFv light chain: HPX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

I
B

Q
B

B
D

J
D

R
D

C
E

K
E

S
E

D
G

L
G

T
G

E
H

M
H

U
H

F
L

N
L

V
L

G
U

O
U

W
U

H
V

P
V

X
V

Envelope glycoprotein gp41

35O22 scFv heavy chain

35O22 scFv light chain

Envelope glycoprotein gp120

3H109L Fab heavy chain

3H109L Fab light chain

CH31 scFv heavy chain

CH31 scFv light chain

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