SMTL ID : 6utk.1

Crystal structure of 438-B11 Fab in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22 at 3.80 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

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

Ligands

15 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.1: 2 residues within 4Å: Chain C: S.26, N.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain D: K.304, N.308, T.368, S.369, S.378 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.368 NAG-NAG-BMA.11: 2 residues within 4Å: Chain D: Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain D: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain D: N.355 Ligands: NAG-NAG-BMA-MAN.8, NAG-NAG-BMA-MAN.8, NAG-NAG-BMA-MAN-MAN-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 2 residues within 4Å: Chain I: S.26, N.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 5 residues within 4Å: Chain J: K.304, N.308, T.368, S.369, S.378 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:T.368 NAG-NAG-BMA.35: 2 residues within 4Å: Chain J: Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 3 residues within 4Å: Chain J: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 4 residues within 4Å: Chain J: N.355 Ligands: NAG-NAG-BMA-MAN.32, NAG-NAG-BMA-MAN.32, NAG-NAG-BMA-MAN-MAN-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.49: 2 residues within 4Å: Chain O: S.26, N.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.53: 5 residues within 4Å: Chain P: K.304, N.308, T.368, S.369, S.378 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:T.368 NAG-NAG-BMA.59: 2 residues within 4Å: Chain P: Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.60: 3 residues within 4Å: Chain P: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.63: 4 residues within 4Å: Chain P: N.355 Ligands: NAG-NAG-BMA-MAN.56, NAG-NAG-BMA-MAN.56, NAG-NAG-BMA-MAN-MAN-MAN.57 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2: 10 residues within 4Å: Chain C: S.95 Chain D: N.271, I.292 Chain F: V.54, V.55, G.56, I.57, Y.58, K.59, Y.113 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26: 10 residues within 4Å: Chain I: S.95 Chain J: N.271, I.292 Chain L: V.54, V.55, G.56, I.57, Y.58, K.59, Y.113 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.50: 10 residues within 4Å: Chain O: S.95 Chain P: N.271, I.292 Chain R: V.54, V.55, G.56, I.57, Y.58, K.59, Y.113 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.3: 4 residues within 4Å: Chain D: T.105, N.107, D.110 Ligands: NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: N.204, T.206, H.321 Ligands: NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 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.27: 4 residues within 4Å: Chain J: T.105, N.107, D.110 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain J: N.204, T.206, H.321 Ligands: NAG.43 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 6 residues within 4Å: Chain J: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.51: 4 residues within 4Å: Chain P: T.105, N.107, D.110 Ligands: NAG.65 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 4 residues within 4Å: Chain P: N.204, T.206, H.321 Ligands: NAG.67 No protein-ligand interaction detected (PLIP) NAG-NAG.58: 6 residues within 4Å: Chain P: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP)

6 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.6: 3 residues within 4Å: Chain D: T.105, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.8: 6 residues within 4Å: Chain D: N.332, S.333, S.334, S.357 Ligands: NAG-NAG-BMA.15, NAG-NAG-BMA.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.30: 3 residues within 4Å: Chain J: T.105, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.32: 6 residues within 4Å: Chain J: N.332, S.333, S.334, S.357 Ligands: NAG-NAG-BMA.39, NAG-NAG-BMA.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.54: 3 residues within 4Å: Chain P: T.105, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.56: 6 residues within 4Å: Chain P: N.332, S.333, S.334, S.357 Ligands: NAG-NAG-BMA.63, NAG-NAG-BMA.63 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- 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-(1-3)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN.7: 19 residues within 4Å: Chain C: S.32, W.33, A.51, A.57, Y.92 Chain D: T.267, H.299, N.301, R.412 Chain F: W.99, R.100, C.102, C.105, Y.107, D.108, Y.112, N.114, D.115, D.118 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.31: 19 residues within 4Å: Chain I: S.32, W.33, A.51, A.57, Y.92 Chain J: T.267, H.299, N.301, R.412 Chain L: W.99, R.100, C.102, C.105, Y.107, D.108, Y.112, N.114, D.115, D.118 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Y.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.55: 19 residues within 4Å: Chain O: S.32, W.33, A.51, A.57, Y.92 Chain P: T.267, H.299, N.301, R.412 Chain R: W.99, R.100, C.102, C.105, Y.107, D.108, Y.112, N.114, D.115, D.118 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:Y.107

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.9: 5 residues within 4Å: Chain D: S.357, G.358, N.361 Ligands: NAG-NAG-BMA.15, NAG-NAG-BMA.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.33: 5 residues within 4Å: Chain J: S.357, G.358, N.361 Ligands: NAG-NAG-BMA.39, NAG-NAG-BMA.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.57: 5 residues within 4Å: Chain P: S.357, G.358, N.361 Ligands: NAG-NAG-BMA.63, NAG-NAG-BMA.63 No protein-ligand interaction detected (PLIP)

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.13: 19 residues within 4Å: Chain A: N.30, F.31, Y.32, H.33, S.52, Y.54, S.55, D.57, N.59, L.109, R.110, D.111, G.112, S.113, T.115 Chain B: H.95, N.96 Chain D: N.58 Chain E: S.17 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.115, B:H.95, A:H.33, A:S.52, A:S.52 NAG-NAG-BMA-MAN-MAN-MAN-MAN.37: 19 residues within 4Å: Chain G: N.30, F.31, Y.32, H.33, S.52, Y.54, S.55, D.57, N.59, L.109, R.110, D.111, G.112, S.113, T.115 Chain H: H.95, N.96 Chain J: N.58 Chain K: S.17 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:H.95, G:T.115, G:H.33, G:S.52, G:S.52 NAG-NAG-BMA-MAN-MAN-MAN-MAN.61: 19 residues within 4Å: Chain M: N.30, F.31, Y.32, H.33, S.52, Y.54, S.55, D.57, N.59, L.109, R.110, D.111, G.112, S.113, T.115 Chain N: H.95, N.96 Chain P: N.58 Chain Q: S.17 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain M Hydrogen bonds: N:H.95, M:T.115, M:H.33, M:S.52, M:S.52

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.14: 9 residues within 4Å: Chain D: K.35, E.181, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.348 NAG-NAG-BMA-MAN-MAN.38: 9 residues within 4Å: Chain J: K.35, E.181, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.42 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.348 NAG-NAG-BMA-MAN-MAN.62: 9 residues within 4Å: Chain P: K.35, E.181, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.66 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.348

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.16: 6 residues within 4Å: Chain B: R.56, G.59, I.60 Chain E: N.92, R.93, N.94 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 6 residues within 4Å: Chain H: R.56, G.59, I.60 Chain K: N.92, R.93, N.94 No protein-ligand interaction detected (PLIP) NAG-NAG.64: 6 residues within 4Å: Chain N: R.56, G.59, I.60 Chain Q: N.92, R.93, N.94 No protein-ligand interaction detected (PLIP)

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

NAG.17: 8 residues within 4Å: Chain D: N.103, N.107, D.110, G.114, E.115, K.117, Y.161 Ligands: NAG-NAG.3 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain D: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.14 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain D: N.246, N.249 Ligands: NAG-NAG.4, NAG-NAG.4 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain D: R.319, N.324, N.325, S.366 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain D: I.365, S.366, N.367 Ligand excluded by PLIP NAG.22: 9 residues within 4Å: Chain A: Y.32, K.106, G.107, L.108, Y.119 Chain E: R.93, E.97, N.101, Q.106 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain E: N.113 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain E: N.87, S.89 Ligand excluded by PLIP NAG.41: 8 residues within 4Å: Chain J: N.103, N.107, D.110, G.114, E.115, K.117, Y.161 Ligands: NAG-NAG.27 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain J: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.38 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain J: N.246, N.249 Ligands: NAG-NAG.28, NAG-NAG.28 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain J: R.319, N.324, N.325, S.366 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain J: I.365, S.366, N.367 Ligand excluded by PLIP NAG.46: 9 residues within 4Å: Chain G: Y.32, K.106, G.107, L.108, Y.119 Chain K: R.93, E.97, N.101, Q.106 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain K: N.113 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain K: N.87, S.89 Ligand excluded by PLIP NAG.65: 8 residues within 4Å: Chain P: N.103, N.107, D.110, G.114, E.115, K.117, Y.161 Ligands: NAG-NAG.51 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain P: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.62 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain P: N.246, N.249 Ligands: NAG-NAG.52, NAG-NAG.52 Ligand excluded by PLIP NAG.68: 4 residues within 4Å: Chain P: R.319, N.324, N.325, S.366 Ligand excluded by PLIP NAG.69: 3 residues within 4Å: Chain P: I.365, S.366, N.367 Ligand excluded by PLIP NAG.70: 9 residues within 4Å: Chain M: Y.32, K.106, G.107, L.108, Y.119 Chain Q: R.93, E.97, N.101, Q.106 Ligand excluded by PLIP NAG.71: 1 residues within 4Å: Chain Q: N.113 Ligand excluded by PLIP NAG.72: 2 residues within 4Å: Chain Q: N.87, S.89 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, S. et al., A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite. Sci Adv (2020)

Release Date

2020-09-23

Peptides

35O22 Fab Heavy Chain: AGM
35O22 Fab Light Chain: BHN
B11 Fab Light Chain: CIO
Envelope glycoprotein gp120: DJP
Envelope glycoprotein gp41: EKQ
B11 Fab Heavy chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

G
D

M
D

B
E

H
E

N
E

C
L

I
L

O
L

D
G

J
G

P
G

E
T

K
T

Q
T

F
H

L
H

R
H

35O22 Fab Heavy Chain

35O22 Fab Light Chain

B11 Fab Light Chain

Envelope glycoprotein gp120

Envelope glycoprotein gp41

B11 Fab Heavy chain

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