SMTL ID : 1w5c.1 (1 other biounit)

Photosystem II from Thermosynechococcus elongatus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-oligomer

Ligands

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 25 residues within 4Å: Chain A: F.119, Y.147, P.150, S.153, F.182, M.183, I.184, F.186, Q.187, I.192, L.193, H.198, G.201, V.202, V.205, F.206, V.283, T.286, I.290 Chain D: L.182, L.205 Ligands: CLA.2, CLA.3, PHO.4, CLA.40 14 PLIP interactions: 3 interactions with chain D, 11 interactions with chain A, Hydrophobic interactions: D:L.182, D:L.182, D:L.205, A:F.119, A:P.150, A:F.186, A:Q.187, A:I.192, A:L.193, A:V.202, A:V.205, A:I.290 Hydrogen bonds: A:S.153 Metal complexes: A:H.198 CLA.2: 15 residues within 4Å: Chain A: V.157, F.158, M.172, I.176, T.179, F.180, F.182, M.183 Chain D: M.198, V.201, A.202, L.209 Ligands: CLA.1, PHO.4, CLA.40 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A, Hydrophobic interactions: D:V.201, D:A.202, D:L.209, A:V.157, A:F.158, A:F.182 CLA.3: 12 residues within 4Å: Chain A: Q.199, V.202, A.203 Chain D: F.157, V.175, I.178, F.179, F.181, L.182 Ligands: CLA.1, CLA.40, PHO.41 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, Hydrophobic interactions: D:F.181, D:L.182, A:V.202 Hydrogen bonds: A:Q.199 CLA.5: 13 residues within 4Å: Chain A: V.35, I.36, P.39, T.40, F.93, P.95, I.96, W.97, Q.113, L.114, H.118 Chain J: X.8, X.14 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:P.39, A:F.93, A:I.96 Hydrogen bonds: A:I.96 pi-Cation interactions: A:H.118 Metal complexes: A:H.118 CLA.11: 5 residues within 4Å: Chain B: D.188, F.190 Chain J: X.226, X.227 Ligands: CLA.12 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:F.190 CLA.12: 13 residues within 4Å: Chain B: F.190, P.192, G.197, V.198, A.200, H.201, A.204, A.205, V.208, F.247, T.255 Ligands: CLA.11, CLA.13 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:F.190, B:F.190, B:P.192, B:A.205, B:V.208 Metal complexes: B:H.201 CLA.13: 16 residues within 4Å: Chain B: R.68, L.69, A.146, L.149, C.150, F.153, L.158, M.166, V.198, H.201, H.202, V.252, T.262 Ligands: CLA.12, CLA.14, CLA.16 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.69, B:L.149, B:F.153, B:F.153 Hydrogen bonds: B:R.68 Salt bridges: B:R.68 pi-Stacking: B:F.153 Metal complexes: B:H.202 CLA.14: 19 residues within 4Å: Chain B: W.33, F.61, F.65, R.68, L.69, V.245, A.248, A.249, V.252, F.451, H.455, F.458, A.459, F.462 Ligands: CLA.13, CLA.15, CLA.17, CLA.21, CLA.23 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.33, B:F.61, B:F.65, B:L.69, B:V.245, B:A.248, B:A.249, B:V.252, B:F.451, B:F.458, B:F.458, B:F.458, B:F.462 Salt bridges: B:R.68 pi-Stacking: B:F.451 Metal complexes: B:H.455 CLA.15: 12 residues within 4Å: Chain B: T.27, V.30, A.31, W.33, A.34, V.62, F.65, M.66, V.96, H.100 Ligands: CLA.14, CLA.16 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:V.30, B:A.31, B:W.33, B:A.34, B:F.65, B:V.96 Hydrogen bonds: B:M.66 Metal complexes: B:H.100 CLA.16: 12 residues within 4Å: Chain B: L.69, G.70, V.71, W.91, G.152, F.153, F.156, H.157, F.162, P.164 Ligands: CLA.13, CLA.15 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.69, B:L.69, B:W.91, B:F.153, B:F.156, B:F.162, B:F.162, B:F.162 Metal complexes: B:H.157 CLA.17: 15 residues within 4Å: Chain B: W.33, M.37, Y.40, G.59, F.61, R.326, T.327, W.450, F.451, A.454, H.455 Chain D: M.199, M.281 Ligands: CLA.14, CLA.23 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:W.33, B:Y.40, B:F.61, B:W.450, B:W.450, B:W.450, B:A.454 pi-Stacking: B:F.61, B:W.450 CLA.18: 16 residues within 4Å: Chain B: T.236, S.239, S.240, A.243, F.246, F.247, F.463, H.466, I.467, T.473, L.474 Chain D: I.123, M.126, L.127, F.130 Ligands: CLA.19 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain D, Hydrophobic interactions: B:F.246, B:F.246, B:F.247, B:F.463, B:I.467, B:L.474, D:I.123, D:I.123, D:M.126, D:F.130 Salt bridges: B:H.466 Metal complexes: B:H.466 CLA.19: 11 residues within 4Å: Chain B: F.139, A.212, F.215, H.216, R.220, P.221, P.222, M.231 Chain J: X.266 Ligands: CLA.18, CLA.20 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:A.212, B:F.215, B:F.215 Salt bridges: B:H.216 Metal complexes: B:H.216 CLA.20: 6 residues within 4Å: Chain B: F.139, H.142, V.237, S.240, S.241 Ligands: CLA.19 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:F.139, B:V.237, B:V.237 pi-Stacking: B:F.139 CLA.21: 13 residues within 4Å: Chain B: L.238, I.242, L.461, F.462, F.464, G.465, W.468, H.469, R.472 Ligands: CLA.14, CLA.22, CLA.23, CLA.24 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.238, B:F.462, B:F.462, B:F.464 Salt bridges: B:R.472 pi-Stacking: B:W.468, B:W.468 Metal complexes: B:H.469 CLA.22: 13 residues within 4Å: Chain B: L.19, A.22, H.23, H.26, E.235, V.237, L.238, S.241, I.242 Ligands: CLA.21, CLA.23, CLA.24, CLA.25 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:A.22, B:H.26, B:V.237, B:L.238 Hydrogen bonds: B:S.241 pi-Stacking: B:H.26 Metal complexes: B:H.23 CLA.23: 12 residues within 4Å: Chain B: H.26, L.29, V.30, W.33, F.458, L.461, F.462 Ligands: CLA.14, CLA.17, CLA.21, CLA.22, CLA.24 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:L.29, B:V.30, B:V.30, B:W.33, B:F.458, B:F.462 CLA.24: 5 residues within 4Å: Chain B: A.22, L.29 Ligands: CLA.21, CLA.22, CLA.23 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:L.29 CLA.25: 14 residues within 4Å: Chain B: I.20, H.23, L.24, T.27, L.106, L.109, A.110, W.113, M.138, I.141, H.142, L.145 Ligands: CLA.22, CLA.26 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:I.20, B:L.106, B:L.109, B:A.110, B:I.141, B:L.145 Hydrogen bonds: B:H.23, B:T.27 CLA.26: 7 residues within 4Å: Chain B: L.24, L.107, A.110, W.113, H.114, Y.117 Ligands: CLA.25 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:L.24, B:L.107, B:A.110 Metal complexes: B:H.114 CLA.27: 14 residues within 4Å: Chain C: T.94, L.95, L.168, G.171, A.172, L.175, V.233, H.237, I.240, F.289, V.296, Y.297 Ligands: CLA.28, CLA.33 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.168, C:A.172, C:L.175, C:V.233, C:I.240, C:I.240, C:F.289, C:V.296 Hydrogen bonds: C:Y.297 Metal complexes: C:H.237 CLA.28: 16 residues within 4Å: Chain C: W.63, H.91, L.279, G.283, A.286, V.290, Y.297, L.426, H.430, L.433, A.434, F.437 Ligands: CLA.27, CLA.29, CLA.30, CLA.36 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:W.63, C:L.279, C:A.286, C:L.426, C:L.433, C:F.437 Salt bridges: C:H.91 Metal complexes: C:H.430 CLA.29: 6 residues within 4Å: Chain C: I.60, V.61, A.64, I.92, H.118 Ligands: CLA.28 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:I.60, C:V.61, C:A.64, C:I.92 Metal complexes: C:H.118 CLA.30: 12 residues within 4Å: Chain A: F.300, F.302 Chain C: W.63, M.67, F.70, G.85, I.87, W.425, S.429, H.430 Chain J: X.306 Ligands: CLA.28 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:W.63, C:F.70, C:I.87, C:W.425, C:W.425, A:F.302 pi-Stacking: C:W.425 CLA.31: 15 residues within 4Å: Chain A: F.33, S.124, G.128, W.131 Chain C: I.265, S.273, Y.274, G.277, A.278, H.441, L.442, A.445, R.449 Ligands: CLA.32, CLA.33 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A, Hydrophobic interactions: C:Y.274, C:L.442, A:F.33, A:W.131, A:W.131, A:W.131 Salt bridges: C:R.449 Metal complexes: C:H.441 pi-Stacking: A:W.131 CLA.32: 13 residues within 4Å: Chain C: L.161, I.243, C.244, G.247, W.250, H.251, P.256, F.257, W.259, A.260, F.264 Ligands: CLA.31, CLA.33 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:L.161, C:L.161, C:I.243, C:A.260, C:F.264 pi-Stacking: C:W.250 Metal complexes: C:H.251 CLA.33: 20 residues within 4Å: Chain C: K.154, M.157, T.158, L.161, H.164, L.168, I.240, C.244, F.264, W.266, Y.271, Y.274, S.275, A.278, L.279, M.282 Ligands: CLA.27, CLA.31, CLA.32, CLA.35 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:M.157, C:L.161, C:L.161, C:L.161, C:L.168, C:L.168, C:I.240, C:F.264, C:Y.271, C:Y.274, C:A.278, C:L.279 Salt bridges: C:H.164 CLA.34: 16 residues within 4Å: Chain C: W.36, A.37, N.39, A.40, L.272, L.276, F.436, F.437, V.439, G.440, W.443, H.444, R.447 Ligands: CLA.35, CLA.36, CLA.37 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:W.36, C:N.39, C:L.272, C:L.272, C:L.276, C:L.276, C:F.437, C:V.439, C:W.443, C:W.443 Hydrogen bonds: C:N.39 Salt bridges: C:R.447 pi-Stacking: C:W.443 Metal complexes: C:H.444 CLA.35: 14 residues within 4Å: Chain C: N.39, I.43, A.52, H.53, H.56, G.268, E.269, Y.271, L.272, S.275, L.276 Ligands: CLA.33, CLA.34, CLA.36 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:N.39, C:I.43, C:A.52, C:H.56, C:E.269, C:Y.271, C:L.272 Hydrogen bonds: C:S.275 Metal complexes: C:H.53 CLA.36: 7 residues within 4Å: Chain C: H.56, L.59, I.60 Ligands: CLA.28, CLA.34, CLA.35, CLA.37 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:I.60 Metal complexes: C:H.56 CLA.37: 11 residues within 4Å: Chain C: R.26, D.27, G.38, N.39, R.41, K.48, A.52, A.133 Chain J: X.316 Ligands: CLA.34, CLA.36 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:A.133 Hydrogen bonds: C:R.41 CLA.38: 10 residues within 4Å: Chain C: L.50, H.53, V.54, A.57, S.145, I.160, F.163, H.164, V.167 Ligands: CLA.39 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:L.50, C:S.145, C:I.160, C:F.163, C:V.167, C:V.167 Metal complexes: C:H.164 CLA.39: 7 residues within 4Å: Chain C: V.124, F.127, G.128, Y.131, H.132, P.137 Ligands: CLA.38 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:F.127, C:F.127, C:Y.131 CLA.40: 23 residues within 4Å: Chain A: M.183, F.206 Chain D: L.122, V.152, F.153, S.155, V.156, F.181, L.182, F.185, Q.186, W.191, H.197, G.200, V.201, V.204, L.279, S.282, V.286 Ligands: CLA.1, CLA.2, CLA.3, PHO.41 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:L.122, D:F.153, D:F.181, D:F.185, D:Q.186, D:W.191, D:V.201, D:V.204, D:L.279, A:F.206 pi-Stacking: D:W.191 Metal complexes: D:H.197 CLA.42: 15 residues within 4Å: Chain D: L.36, P.39, C.40, L.43, L.89, L.90, L.91, L.92, W.93, W.104, T.112, F.113, L.116, H.117 Chain J: X.242 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:L.36, D:W.93, D:W.93, D:L.116 Hydrogen bonds: D:L.92 Salt bridges: D:H.117 pi-Stacking: D:F.113 Metal complexes: D:H.117

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.4: 25 residues within 4Å: Chain A: L.41, A.44, T.45, F.48, I.115, F.119, Y.126, Q.130, A.146, Y.147, P.150, M.172, L.174, G.175, I.176, P.279, V.283 Chain D: L.205, A.208, L.209, A.212, I.213, F.257 Ligands: CLA.1, CLA.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.41, A:A.44, A:F.48, A:I.115, A:A.146, A:Y.147, A:Y.147, A:P.150, A:P.279, D:L.205, D:A.212 Hydrogen bonds: A:Q.130, A:Y.147 PHO.41: 23 residues within 4Å: Chain A: F.206, A.209, L.210, A.213, M.214, I.259 Chain D: A.41, I.114, G.118, L.122, F.125, N.142, A.145, F.146, A.148, P.149, F.153, F.173, P.275, V.276, L.279 Ligands: CLA.3, CLA.40 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.114, D:L.122, D:F.125, D:A.145, D:A.148, D:F.153, D:F.173, D:P.275, D:L.279, A:F.206, A:L.210, A:L.210 Hydrogen bonds: D:N.142 pi-Stacking: D:F.146

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.6: 3 residues within 4Å: Chain A: D.170, E.333 Ligands: MN.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.170, A:E.333, A:E.333 MN.7: 4 residues within 4Å: Chain A: E.189, H.332 Ligands: MN.8, MN.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.332 MN.8: 5 residues within 4Å: Chain A: E.189, E.333 Ligands: MN.6, MN.7, MN.10 No protein-ligand interaction detected (PLIP) MN.10: 2 residues within 4Å: Ligands: MN.7, MN.8 No protein-ligand interaction detected (PLIP)

1 x FE2: FE (II) ION(Non-covalent)

FE2.9: 4 residues within 4Å: Chain A: H.215, H.272 Chain D: H.214, H.268 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:H.215, A:H.272, D:H.214, D:H.268

1 x PL9: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE(Non-covalent)

PL9.43: 5 residues within 4Å: Chain D: T.217, A.249, W.253, F.261, L.267 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.217, D:A.249, D:L.267

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.44: 7 residues within 4Å: Chain E: Y.19, H.23, T.26, I.27 Chain F: W.19, H.23, A.26 10 PLIP interactions: 5 interactions with chain F, 5 interactions with chain E, Hydrophobic interactions: F:A.26, E:T.26, E:I.27 pi-Stacking: F:W.19, F:H.23, F:H.23, E:Y.19, E:H.23, E:H.23 Metal complexes: F:H.23

1 x BCR: BETA-CAROTENE(Non-covalent)

BCR.45: 10 residues within 4Å: Chain D: Y.42, L.43, G.46, L.49, F.101, F.113 Chain F: P.28, T.29, F.32, L.33 10 PLIP interactions: 5 interactions with chain F, 5 interactions with chain D Hydrophobic interactions: F:P.28, F:T.29, F:F.32, F:F.32, F:F.32, D:Y.42, D:L.43, D:L.49, D:L.49, D:F.101

1 x HEC: HEME C(Covalent)

HEC.46: 23 residues within 4Å: Chain I: A.62, C.63, S.65, C.66, H.67, T.74, L.78, D.79, L.80, T.84, L.85, A.88, R.92, L.98, Y.101, M.102, Y.108, I.114, H.118, P.119, M.130, I.141, I.145 17 PLIP interactions: 17 interactions with chain I, Hydrophobic interactions: I:A.62, I:L.78, I:L.80, I:L.98, I:Y.101, I:P.119, I:I.141, I:I.145 pi-Stacking: I:H.67, I:H.67, I:Y.101, I:H.118, I:H.118, I:H.118, I:H.118 Metal complexes: I:H.67, I:H.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biesiadka, J. et al., Crystal Structure of Cyanobacterial Photosystem II at 3.2 A Resolution: A Closer Look at the Mn- Cluster. Phys.Chem.Chem.Phys. (2004)

Release Date

2004-12-21

Peptides

PHOTOSYSTEM Q(B) PROTEIN 1: A
PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN: B
PHOTOSYSTEM II CP43 PROTEIN: C
PHOTOSYSTEM II REACTION CENTER D2 PROTEIN: D
CYTOCHROME B559 ALPHA SUBUNIT: E
CYTOCHROME B559 BETA SUBUNIT: F
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE: G
PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN: H
CYTOCHROME C-550: I
UNASSIGNED SUBUNITS: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
O

H
U

I
V

J
X

Membrane

We predict this structure to be a membrane protein.
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PHOTOSYSTEM Q(B) PROTEIN 1

PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN

PHOTOSYSTEM II CP43 PROTEIN

PHOTOSYSTEM II REACTION CENTER D2 PROTEIN

CYTOCHROME B559 ALPHA SUBUNIT

CYTOCHROME B559 BETA SUBUNIT

PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE

PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN

CYTOCHROME C-550

UNASSIGNED SUBUNITS

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