SMTL ID : 6opa.1

Crystal structure of bovine Fab NC-Cow1 in complex with HIV-1 BG505 SOSIP.664, and human Fabs 35022 and PGT128

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.08 Å

Oligo State

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

Ligands

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.1: 19 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 Chain C: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain D: H.95, N.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.115, C:D.111, C:H.33 NAG-NAG-BMA-MAN-MAN-MAN-MAN.16: 19 residues within 4Å: Chain I: E.57, N.58 Chain J: G.16, S.17 Chain K: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain L: H.95, N.96 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:T.115, K:D.111, K:H.33 NAG-NAG-BMA-MAN-MAN-MAN-MAN.31: 19 residues within 4Å: Chain Q: E.57, N.58 Chain R: G.16, S.17 Chain S: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain T: H.95, N.96 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:T.115, S:D.111, S:H.33

6 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 A: N.103, K.159, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: N.204, T.206, S.244, E.245, I.247 Chain C: P.77, V.78 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain I: N.103, K.159, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain I: N.204, T.206, S.244, E.245, I.247 Chain K: P.77, V.78 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain Q: N.103, K.159, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 7 residues within 4Å: Chain Q: N.204, T.206, S.244, E.245, I.247 Chain S: P.77, V.78 No protein-ligand interaction detected (PLIP)

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.3: 4 residues within 4Å: Chain A: N.118, Y.135, D.290 Chain F: R.112 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 6 residues within 4Å: Chain A: N.332, S.333, T.341, N.355, T.356, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain I: N.118, Y.135, D.290 Chain N: R.112 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 6 residues within 4Å: Chain I: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 6 residues within 4Å: Chain I: N.332, S.333, T.341, N.355, T.356, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 4 residues within 4Å: Chain Q: N.118, Y.135, D.290 Chain V: R.112 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 6 residues within 4Å: Chain Q: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 6 residues within 4Å: Chain Q: N.332, S.333, T.341, N.355, T.356, S.357 No protein-ligand interaction detected (PLIP)

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.5: 7 residues within 4Å: Chain A: V.144, R.162, I.164, N.167, T.168 Chain H: Q.119, Q.120 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:Q.119, H:Q.120 Hydrogen bonds: H:Q.120, H:Q.120 NAG-NAG-BMA-MAN.8: 8 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, S.381, R.412 Ligands: NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.20: 7 residues within 4Å: Chain I: V.144, R.162, I.164, N.167, T.168 Chain P: Q.119, Q.120 4 PLIP interactions: 4 interactions with chain P Hydrophobic interactions: P:Q.119, P:Q.120 Hydrogen bonds: P:Q.120, P:Q.120 NAG-NAG-BMA-MAN.23: 8 residues within 4Å: Chain I: Q.263, N.265, N.301, V.302, S.303, S.381, R.412 Ligands: NAG-NAG-BMA-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.35: 7 residues within 4Å: Chain Q: V.144, R.162, I.164, N.167, T.168 Chain X: Q.119, Q.120 4 PLIP interactions: 4 interactions with chain X Hydrophobic interactions: X:Q.119, X:Q.120 Hydrogen bonds: X:Q.120, X:Q.120 NAG-NAG-BMA-MAN.38: 8 residues within 4Å: Chain Q: Q.263, N.265, N.301, V.302, S.303, S.381, R.412 Ligands: NAG-NAG-BMA-MAN-MAN.40 No protein-ligand interaction detected (PLIP)

12 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.7: 9 residues within 4Å: Chain A: S.179, E.181, P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG-BMA-MAN.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN.9: 8 residues within 4Å: Chain A: N.271, I.292 Chain F: A.30, C.32, H.55, A.57, S.58, T.81 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.55, F:T.81, F:R.62 NAG-NAG-BMA-MAN-MAN.10: 11 residues within 4Å: Chain A: N.265, T.267, R.296, H.299, N.301, R.412 Chain E: N.91, W.92 Chain F: Y.59, D.115 Ligands: NAG-NAG-BMA-MAN.8 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:N.91, A:R.296, A:R.296 NAG-NAG-BMA-MAN-MAN.13: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 9 residues within 4Å: Chain I: S.179, E.181, P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG-BMA-MAN.27 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.348 NAG-NAG-BMA-MAN-MAN.24: 8 residues within 4Å: Chain I: N.271, I.292 Chain N: A.30, C.32, H.55, A.57, S.58, T.81 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:H.55, N:T.81, N:R.62 NAG-NAG-BMA-MAN-MAN.25: 11 residues within 4Å: Chain I: N.265, T.267, R.296, H.299, N.301, R.412 Chain M: N.91, W.92 Chain N: Y.59, D.115 Ligands: NAG-NAG-BMA-MAN.23 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain I Hydrogen bonds: M:N.91, I:R.296, I:R.296 NAG-NAG-BMA-MAN-MAN.28: 3 residues within 4Å: Chain I: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.37: 9 residues within 4Å: Chain Q: S.179, E.181, P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG-BMA-MAN.42 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:G.348 NAG-NAG-BMA-MAN-MAN.39: 8 residues within 4Å: Chain Q: N.271, I.292 Chain V: A.30, C.32, H.55, A.57, S.58, T.81 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:H.55, V:T.81, V:R.62 NAG-NAG-BMA-MAN-MAN.40: 11 residues within 4Å: Chain Q: N.265, T.267, R.296, H.299, N.301, R.412 Chain U: N.91, W.92 Chain V: Y.59, D.115 Ligands: NAG-NAG-BMA-MAN.38 3 PLIP interactions: 1 interactions with chain U, 2 interactions with chain Q Hydrogen bonds: U:N.91, Q:R.296, Q:R.296 NAG-NAG-BMA-MAN-MAN.43: 3 residues within 4Å: Chain Q: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP)

3 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.12: 3 residues within 4Å: Chain A: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.27: 3 residues within 4Å: Chain I: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.42: 3 residues within 4Å: Chain Q: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.37 No protein-ligand interaction detected (PLIP)

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

NAG.14: 2 residues within 4Å: Chain B: N.100, S.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.102 NAG.15: 4 residues within 4Å: Chain A: E.2 Chain B: N.105, N.107 Chain D: G.59 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.59 NAG.29: 2 residues within 4Å: Chain J: N.100, S.102 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.102 NAG.30: 4 residues within 4Å: Chain I: E.2 Chain J: N.105, N.107 Chain L: G.59 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.59 NAG.44: 2 residues within 4Å: Chain R: N.100, S.102 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:S.102 NAG.45: 4 residues within 4Å: Chain Q: E.2 Chain R: N.105, N.107 Chain T: G.59 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:G.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanfield, R.L. et al., Structural basis of broad HIV neutralization by a vaccine-induced cow antibody. Sci Adv (2020)

Release Date

2020-04-01

Peptides

Envelope glycoprotein gp160: AIQ
Envelope glycoprotein gp41: BJR
Fab 35022 heavy chain: CKS
Fab 35022 light chain: DLT
Fab PGT128 light chain: EMU
Fab PGT128 heavy chain: FNV
Fab NC-Cow1 light chain: GOW
Fab NC-Cow1 heavy chain: HPX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

I
G

Q
G

B
B

J
B

R
B

C
F

K
F

S
F

D
I

L
I

T
I

E
J

M
J

U
J

F
K

N
K

V
K

G
R

O
R

W
R

H
S

P
S

X
S

Envelope glycoprotein gp160

Envelope glycoprotein gp41

Fab 35022 heavy chain

Fab 35022 light chain

Fab PGT128 light chain

Fab PGT128 heavy chain

Fab NC-Cow1 light chain

Fab NC-Cow1 heavy chain

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