SMTL ID : 6nnf.1

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to VRC01 FR3-03 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.5 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 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: 19 residues within 4Å: Chain A: S.17 Chain B: N.30, F.31, 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 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.112, B:T.115, C:H.96, B:D.111, B:G.112, B:S.113, B:H.33, B:S.52, B:S.52 Hydrophobic interactions: B:T.115 NAG-NAG-BMA-MAN-MAN-MAN.17: 19 residues within 4Å: Chain I: S.17 Chain J: N.30, F.31, 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 5 PLIP interactions: 1 interactions with chain K, 4 interactions with chain J Hydrogen bonds: K:H.96, J:G.112, J:T.115, J:D.111, J:G.112, J:S.113, J:H.33, J:S.52, J:S.52 Hydrophobic interactions: J:T.115 NAG-NAG-BMA-MAN-MAN-MAN.33: 19 residues within 4Å: Chain Q: S.17 Chain R: N.30, F.31, 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 5 PLIP interactions: 4 interactions with chain R, 1 interactions with chain S Hydrogen bonds: R:G.112, R:T.115, S:H.96, R:D.111, R:G.112, R:S.113, R:H.33, R:S.52, R:S.52 Hydrophobic interactions: R:T.115

21 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: T.102, N.103, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain D: V.144, R.162, N.167 Chain G: Q.76 Chain L: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: N.246, T.248 Chain H: Y.28, G.29, R.64 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.64 NAG-NAG.7: 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.8: 3 residues within 4Å: Chain D: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain D: N.355 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain D: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain L: T.102, N.103, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain L: V.144, R.162, N.167 Chain O: Q.76 Chain T: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain L: N.246, T.248 Chain P: Y.28, G.29, R.64 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:R.64 NAG-NAG.23: 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.24: 3 residues within 4Å: Chain L: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain L: N.355 Ligands: NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain L: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain T: T.102, N.103, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 5 residues within 4Å: Chain D: R.278 Chain T: V.144, R.162, N.167 Chain W: Q.76 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain T: N.246, T.248 Chain X: Y.28, G.29, R.64 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:R.64 NAG-NAG.39: 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.40: 3 residues within 4Å: Chain T: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 2 residues within 4Å: Chain T: N.355 Ligands: NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 5 residues within 4Å: Chain T: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.37 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: 2 residues within 4Å: Chain D: N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 2 residues within 4Å: Chain L: N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.35: 2 residues within 4Å: Chain T: N.118, Y.135 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.5: 9 residues within 4Å: Chain D: E.181, P.182, V.224, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.348 NAG-NAG-BMA-MAN.21: 9 residues within 4Å: Chain L: E.181, P.182, V.224, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.27 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.348 NAG-NAG-BMA-MAN.37: 9 residues within 4Å: Chain T: E.181, P.182, V.224, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.43 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.9: 22 residues within 4Å: Chain D: T.267, R.296, H.299, N.301, T.383, R.412 Chain E: Q.100, G.101, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain F: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.296, D:R.296, E:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.25: 22 residues within 4Å: Chain L: T.267, R.296, H.299, N.301, T.383, R.412 Chain M: Q.100, G.101, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain N: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain M Hydrogen bonds: L:R.296, L:R.296, M:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.41: 22 residues within 4Å: Chain T: T.267, R.296, H.299, N.301, T.383, R.412 Chain U: Q.100, G.101, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain V: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 3 PLIP interactions: 1 interactions with chain U, 2 interactions with chain T Hydrogen bonds: U:V.108, T:R.296, T:R.296

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

NAG.12: 1 residues within 4Å: Chain A: N.100 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: E.123, N.126 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain D: N.204, T.206, S.244, E.245 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain D: N.332, T.341, N.355, S.357 Ligands: NAG-NAG.10, NAG-NAG.10 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain I: N.100 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain I: E.123, N.126 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain L: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain L: N.204, T.206, S.244, E.245 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain L: N.332, T.341, N.355, S.357 Ligands: NAG-NAG.26, NAG-NAG.26 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain Q: N.100 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain Q: E.123, N.126 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain T: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain T: N.204, T.206, S.244, E.245 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain T: N.332, T.341, N.355, S.357 Ligands: NAG-NAG.42, NAG-NAG.42 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
VRC01 FR3-03 heavy chain: GOW
VRC01 FR3-03 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

VRC01 FR3-03 heavy chain

VRC01 FR3-03 light chain

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