SMTL ID : 4ydk.1

Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex with HIV-1 clade AE strain 93TH057 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 8 residues within 4Å: Chain A: N.118, T.120, G.121, P.122, I.156, S.158, L.161, H.220 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118, A:H.220 NAG.2: 5 residues within 4Å: Chain A: H.42, N.113, K.115, N.125, E.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.42, A:N.125, A:E.151 NAG.3: 11 residues within 4Å: Chain A: P.96, K.136, V.138, L.145, N.146, F.243, R.246, C.306, V.307, S.308 Ligands: PEG.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308, A:S.308 Water bridges: A:R.246, A:N.305, A:V.307 NAG.4: 4 residues within 4Å: Chain A: N.160, T.162, N.163 Ligands: PEG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.160 Water bridges: A:N.163 NAG.5: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.154, A:Q.212 NAG.6: 6 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, N.305, V.307 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:N.179, A:T.181 NAG.7: 4 residues within 4Å: Chain A: N.202, T.204, K.205, K.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.202, A:K.208 NAG.8: 6 residues within 4Å: Chain A: L.236, T.239, M.240, N.253, T.255 Ligands: PEG.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253 Water bridges: A:T.239 NAG.9: 7 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.262, K.269, C.271 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:K.269 NAG.10: 6 residues within 4Å: Chain A: G.147, L.149, S.175, E.177, N.309 Ligands: PEG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.309

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 9 residues within 4Å: Chain A: T.162, N.163, N.164, A.165, R.317 Chain B: Y.102 Chain C: F.49, N.53 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.164 PEG.12: 8 residues within 4Å: Chain A: K.136, N.146, E.177, V.307, S.308, N.309 Ligands: NAG.3, NAG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.136 PEG.13: 4 residues within 4Å: Chain A: N.253, P.278, K.280 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253 PEG.14: 9 residues within 4Å: Chain A: A.12, T.34, D.35, P.38, H.100, Q.130, C.131, T.132, H.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.35, A:H.100, A:Q.130 Water bridges: A:G.134 PEG.21: 12 residues within 4Å: Chain A: T.80, G.81, G.290, T.291, G.292 Chain B: N.30, A.53, H.54, G.55, R.72, H.74, Y.108 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:H.54, B:R.72, B:R.72, A:G.81 PEG.25: 8 residues within 4Å: Chain C: A.84, N.85, W.103, D.105, R.142, E.165, Q.166, Y.173 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.173 PEG.26: 9 residues within 4Å: Chain C: S.10, L.11, S.12, W.103, D.105, Y.140, P.141, R.142, E.143 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.10, C:S.12, C:D.105, C:E.143 Water bridges: C:R.142

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 6 residues within 4Å: Chain A: C.76, V.77, K.86, Q.87, A.88, C.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.76, A:Q.87, A:C.89 GOL.17: 2 residues within 4Å: Chain A: V.84, K.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.86 Water bridges: A:V.84 GOL.18: 14 residues within 4Å: Chain A: C.112, N.113, D.114, K.115, N.116, F.117, A.150, E.151, E.152, I.155, R.157, H.171, Y.345, K.346 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:C.112, A:K.115, A:F.117, A:E.151, A:R.157, A:Y.345, A:Y.345 Water bridges: A:E.152 GOL.19: 9 residues within 4Å: Chain A: T.8, L.9, F.10, C.11, W.26, A.30, Q.60, D.64, Y.101 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.9, A:Q.60, A:D.64 Water bridges: A:C.11, A:D.64, A:S.67 GOL.20: 9 residues within 4Å: Chain A: W.53, E.159, K.166, T.167, N.335, D.338, R.341 Chain B: E.104, G.105 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.159, A:T.167, A:T.167, A:N.335, A:D.338 Water bridges: B:G.105 GOL.22: 5 residues within 4Å: Chain B: F.11, S.131, T.132, F.162, P.163 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.132, B:T.132 GOL.23: 6 residues within 4Å: Chain B: N.31, Y.32, V.99, T.100, F.101, E.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.101, B:F.101 Water bridges: B:N.31, B:Y.32 GOL.24: 8 residues within 4Å: Chain B: G.9, G.10, F.11, L.124, I.126, P.163, E.164, P.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.164 Water bridges: B:L.124 GOL.27: 9 residues within 4Å: Chain C: Q.37, K.45, L.47, V.58, S.59, R.61, F.62, E.81, D.82 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.37, C:K.45, C:S.59, C:D.82 GOL.28: 7 residues within 4Å: Chain C: T.197, H.198, Q.199, L.201, S.202, S.203, P.204 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Q.199 GOL.29: 14 residues within 4Å: Chain B: L.157, F.182, P.183, A.184, V.185, S.193, L.194, S.195 Chain C: Q.160, E.161, S.162, S.176, S.177, T.178 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.195, C:S.162, C:S.162, C:S.176, C:T.178 GOL.30: 6 residues within 4Å: Chain C: S.12, R.107, V.110, Y.140, P.141, Q.199 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.12, C:R.107, C:Q.199 GOL.31: 7 residues within 4Å: Chain B: V.179, H.180, T.181 Chain C: T.164, E.165, Q.166, D.167 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Water bridges: C:E.165, C:D.167, C:S.168, C:S.174, B:V.179, B:T.181 Hydrogen bonds: B:H.180

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.16: 6 residues within 4Å: Chain A: R.195, K.280, K.282, Q.283, I.284, M.295 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.283, A:I.284 Water bridges: A:R.195, A:R.195, A:K.282, A:K.282 Salt bridges: A:R.195, A:K.280, A:K.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell (2015)

Release Date

2015-06-03

Peptides

Envelope glycoprotein gp160,Envelope glycoprotein gp160: A
HEAVY CHAIN OF ANTIBODY C38-VRC16.01: B
LIGHT CHAIN OF ANTIBODY C38-VRC16.01: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

Envelope glycoprotein gp160,Envelope glycoprotein gp160

HEAVY CHAIN OF ANTIBODY C38-VRC16.01

LIGHT CHAIN OF ANTIBODY C38-VRC16.01

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