SMTL ID : 8ucd.1

Cryo-EM structure of human STEAP1 in complex with AMG 509 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

3 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.1: 18 residues within 4Å: Chain A: Q.70, W.71, K.162, Q.163, L.166, F.169, F.170, V.173, I.177, V.235, P.239 Chain B: A.228, A.231, V.235, V.241, S.244 Ligands: LBN.3, LBN.5 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.166, A:L.166, A:F.169, A:F.170, A:F.170, A:V.173, A:I.177, A:V.235, B:A.228, B:A.231, B:V.235 Hydrogen bonds: A:Q.70, A:W.71, A:Q.163 Salt bridges: A:K.162, A:K.162 LBN.3: 19 residues within 4Å: Chain A: A.228, A.231, L.232, V.235, V.241, S.244 Chain B: I.177 Chain C: Q.70, W.71, K.162, Q.163, L.166, F.170, V.173, I.177, V.235, I.238, P.239 Ligands: LBN.1 14 PLIP interactions: 6 interactions with chain A, 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:A.228, A:A.231, A:L.232, A:V.235, A:V.241, C:W.71, C:L.166, C:F.170, C:I.177, C:V.235, C:I.238, B:I.177 Hydrogen bonds: A:S.244 Salt bridges: C:K.162 LBN.5: 19 residues within 4Å: Chain B: Q.70, W.71, K.162, F.169, F.170, V.173, I.177, V.235, S.237, I.238, P.239 Chain C: I.224, L.227, A.228, A.231, L.232, T.236, V.241 Ligands: LBN.1 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.169, B:F.169, B:V.173, B:I.177, B:V.235, B:I.238, C:L.227, C:A.231 Hydrogen bonds: B:Q.70, B:Q.163 Salt bridges: B:K.162

3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 13 residues within 4Å: Chain A: L.126, V.129, Y.130, G.133, Q.140, R.161, K.162, G.165, L.233, S.237, H.251, Q.254, S.255 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.126, A:L.233 Hydrogen bonds: A:Q.140, A:S.237 Salt bridges: A:R.161, A:H.251, A:K.305 FAD.6: 12 residues within 4Å: Chain B: L.126, V.129, Y.130, G.133, R.161, K.162, G.165, L.233, S.237, H.251, Q.254, S.255 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.126, B:L.233 Hydrogen bonds: B:S.237, B:Q.254 Salt bridges: B:R.161, B:R.161, B:H.251 FAD.8: 10 residues within 4Å: Chain C: L.126, V.129, Y.130, R.161, K.162, G.165, L.233, S.237, H.251, Q.254 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.126, C:L.233 Hydrogen bonds: C:R.161, C:S.237, C:Q.254 Salt bridges: C:R.161, C:K.305

3 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.4: 13 residues within 4Å: Chain A: K.116, P.119, S.122, H.175, A.176, S.179, G.223, I.224, L.227, H.268, A.269, F.272, T.290 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:P.119, A:P.119, A:A.176, A:I.224, A:L.227, A:A.269, A:F.272 Hydrogen bonds: A:Y.182 Salt bridges: A:K.116, A:K.116 Metal complexes: A:H.175, A:H.268 HEM.7: 14 residues within 4Å: Chain B: K.116, P.119, H.175, A.176, S.179, G.223, I.224, L.227, L.230, H.268, A.269, F.272, T.290, F.291 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:P.119, B:A.176, B:I.224, B:L.227, B:L.230, B:A.269, B:F.272 Salt bridges: B:K.116, B:K.116 Metal complexes: B:H.175, B:H.268 HEM.9: 12 residues within 4Å: Chain C: K.116, P.119, H.175, A.176, S.179, G.223, I.224, L.227, H.268, F.272, T.290, F.291 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:P.119, C:A.176, C:I.224, C:L.227, C:F.272 Salt bridges: C:K.116, C:K.116 Metal complexes: C:H.175, C:H.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nolan-Stevaux, O. et al., AMG 509 (Xaluritamig), an Anti-STEAP1 XmAb 2+1 T-cell Redirecting Immune Therapy with Avidity-Dependent Activity against Prostate Cancer. Cancer Discov (2024)

Release Date

2023-11-22

Peptides

Metalloreductase STEAP1: ABC
AMG 509 anti-STEAP1 Fab, heavy chain: D
AMG 509 anti-STEAP1 Fab, light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Membrane

We predict this structure to be a membrane protein.
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Metalloreductase STEAP1

AMG 509 anti-STEAP1 Fab, heavy chain

AMG 509 anti-STEAP1 Fab, light chain