SMTL ID : 6hcy.1

human STEAP4 bound to NADP, FAD, heme and Fe(III)-NTA.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 18 residues within 4Å: Chain A: G.26, T.27, G.28, D.29, F.30, S.49, R.50, Y.67, A.80, I.81, H.82, H.85, I.104, S.105, N.106, N.135, I.137, A.139 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.30 Hydrogen bonds: A:T.27, A:T.27, A:D.29, A:D.29, A:F.30, A:R.50, A:Y.67, A:I.81, A:H.85, A:N.106, A:N.106, A:A.139 Salt bridges: A:R.50, A:H.82, A:H.82 pi-Stacking: A:H.85 pi-Cation interactions: A:R.50 NAP.6: 18 residues within 4Å: Chain B: G.26, T.27, G.28, D.29, F.30, S.49, R.50, Y.67, A.80, I.81, H.82, H.85, I.104, S.105, N.106, N.135, I.137, A.139 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.30 Hydrogen bonds: B:T.27, B:T.27, B:D.29, B:D.29, B:F.30, B:R.50, B:Y.67, B:I.81, B:H.85, B:N.106, B:N.106, B:A.139 Salt bridges: B:R.50, B:H.82, B:H.82 pi-Stacking: B:H.85 pi-Cation interactions: B:R.50 NAP.11: 18 residues within 4Å: Chain C: G.26, T.27, G.28, D.29, F.30, S.49, R.50, Y.67, A.80, I.81, H.82, H.85, I.104, S.105, N.106, N.135, I.137, A.139 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:F.30 Hydrogen bonds: C:T.27, C:T.27, C:D.29, C:D.29, C:F.30, C:R.50, C:Y.67, C:I.81, C:H.85, C:N.106, C:N.106, C:A.139 Salt bridges: C:R.50, C:H.82, C:H.82 pi-Stacking: C:H.85 pi-Cation interactions: C:R.50

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

HEM.2: 18 residues within 4Å: Chain A: R.245, P.248, I.249, A.251, L.252, H.304, V.305, T.308, Y.348, G.352, I.353, F.356, C.394, H.397, T.398, Y.401, Y.420 Chain C: V.310 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:P.248, A:P.248, A:A.251, A:V.305, A:T.308, A:Y.348, A:F.356, A:Y.401, C:V.310 Salt bridges: A:R.245 Metal complexes: A:H.304, A:H.397 HEM.7: 19 residues within 4Å: Chain A: V.310, I.313 Chain B: R.245, P.248, I.249, A.251, L.252, H.304, V.305, T.308, Y.348, G.352, I.353, F.356, C.394, H.397, T.398, Y.401, Y.420 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:P.248, B:P.248, B:A.251, B:V.305, B:T.308, B:Y.348, B:F.356, B:Y.401, A:V.310, A:I.313 Salt bridges: B:R.245 Metal complexes: B:H.304, B:H.397 HEM.12: 18 residues within 4Å: Chain B: V.310 Chain C: R.245, P.248, I.249, A.251, L.252, H.304, V.305, T.308, Y.348, G.352, I.353, F.356, C.394, H.397, T.398, Y.401, Y.420 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:P.248, C:P.248, C:A.251, C:V.305, C:T.308, C:Y.348, C:F.356, C:Y.401, B:V.310 Salt bridges: C:R.245 Metal complexes: C:H.304, C:H.397

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

FAD.3: 21 residues within 4Å: Chain A: L.255, V.258, Y.259, G.262, A.266, Q.269, K.275, R.290, K.291, G.294, L.295, F.359, L.362, S.366, F.379, Q.383, S.384, Y.388, R.450 Chain C: W.140, D.148 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.255, A:L.295, A:F.359, A:L.362, A:L.362 Hydrogen bonds: A:Y.259, A:Y.259, A:G.262, A:G.262, A:A.265, A:R.290, A:Q.383, A:S.384, A:Y.388, C:D.148, C:D.148 Salt bridges: A:R.290, A:R.290 pi-Stacking: C:W.140, C:W.140 FAD.8: 21 residues within 4Å: Chain A: W.140, D.148 Chain B: L.255, V.258, Y.259, G.262, A.266, Q.269, K.275, R.290, K.291, G.294, L.295, F.359, L.362, S.366, F.379, Q.383, S.384, Y.388, R.450 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.255, B:L.295, B:F.359, B:L.362, B:L.362 Hydrogen bonds: B:Y.259, B:Y.259, B:G.262, B:G.262, B:A.265, B:R.290, B:Q.383, B:S.384, B:Y.388, A:D.148, A:D.148 Salt bridges: B:R.290, B:R.290 pi-Stacking: A:W.140, A:W.140 FAD.13: 21 residues within 4Å: Chain B: W.140, D.148 Chain C: L.255, V.258, Y.259, G.262, A.266, Q.269, K.275, R.290, K.291, G.294, L.295, F.359, L.362, S.366, F.379, Q.383, S.384, Y.388, R.450 20 PLIP interactions: 16 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.255, C:L.295, C:F.359, C:L.362, C:L.362 Hydrogen bonds: C:Y.259, C:Y.259, C:G.262, C:G.262, C:A.265, C:R.290, C:Q.383, C:S.384, C:Y.388, B:D.148, B:D.148 Salt bridges: C:R.290, C:R.290 pi-Stacking: B:W.140, B:W.140

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

NAG.4: 4 residues within 4Å: Chain A: W.319, N.323 Chain B: E.334, N.335 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.334 NAG.9: 4 residues within 4Å: Chain B: W.319, N.323 Chain C: E.334, N.335 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.334 NAG.14: 4 residues within 4Å: Chain A: E.334, N.335 Chain C: W.319, N.323 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.334

3 x 44E: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate(Non-covalent)

44E.5: 12 residues within 4Å: Chain A: F.197, W.200, F.204, K.291, Q.292, L.295, G.363, S.366, L.367 Chain B: I.364, V.370, V.374 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.197, A:F.197, A:F.204, A:L.295 Hydrogen bonds: A:Q.292 Salt bridges: A:K.291, A:K.291 44E.10: 12 residues within 4Å: Chain B: F.197, W.200, F.204, K.291, Q.292, L.295, G.363, S.366, L.367 Chain C: I.364, V.370, V.374 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.197, B:F.197, B:F.204, B:L.295, C:I.364 Hydrogen bonds: B:Q.292 Salt bridges: B:K.291, B:K.291 44E.15: 12 residues within 4Å: Chain A: I.364, V.370, V.374 Chain C: F.197, W.200, F.204, K.291, Q.292, L.295, G.363, S.366, L.367 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:I.364, C:F.197, C:F.197, C:F.204, C:L.295 Hydrogen bonds: C:Q.292 Salt bridges: C:K.291, C:K.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oosterheert, W. et al., Cryo-EM structures of human STEAP4 reveal mechanism of iron(III) reduction. Nat Commun (2018)

Release Date

2018-10-24

Peptides

Metalloreductase STEAP4: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Membrane

We predict this structure to be a membrane protein.
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Metalloreductase STEAP4

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