SMTL ID : 1izl.1

Crystal Structure of Photosystem II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: A.344 Ligands: MN.2, MN.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.344 MN.2: 4 residues within 4Å: Chain A: E.333 Ligands: MN.1, MN.3, MN.4 No protein-ligand interaction detected (PLIP) MN.3: 3 residues within 4Å: Chain A: D.170, E.333 Ligands: MN.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.170 MN.4: 5 residues within 4Å: Chain A: E.189, E.333, A.344 Ligands: MN.1, MN.2 No protein-ligand interaction detected (PLIP) MN.49: 3 residues within 4Å: Chain O: A.344 Ligands: MN.50, MN.52 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:A.344 MN.50: 4 residues within 4Å: Chain O: E.333 Ligands: MN.49, MN.51, MN.52 No protein-ligand interaction detected (PLIP) MN.51: 2 residues within 4Å: Chain O: D.170 Ligands: MN.50 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.170 MN.52: 5 residues within 4Å: Chain O: E.189, E.333, A.344 Ligands: MN.49, MN.50 No protein-ligand interaction detected (PLIP)

72 x CLA: CHLOROPHYLL A(Non-covalent)(Covalent)(Non-functional Binders)

CLA.5: 9 residues within 4Å: Chain A: F.182, M.183, F.186, Q.187, G.201, V.202, F.206 Ligands: CLA.39, CLA.40 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:F.186, A:Q.187, A:F.206 CLA.6: 6 residues within 4Å: Chain A: F.158, G.178, F.182 Chain D: V.201 Ligands: CLA.39, PHO.41 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:F.158, A:F.182 CLA.8: 9 residues within 4Å: Chain A: I.36, P.39, H.92, Y.94, P.95, L.114, H.118, L.121 Ligands: CLA.9 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:P.39, A:P.95, A:L.114, A:L.121 CLA.9: 3 residues within 4Å: Chain A: L.120 Ligands: CLA.8, CLA.29 1 PLIP interactions: 1 interactions with chain A, Hydrophobic interactions: A:L.120 CLA.10: 2 residues within 4Å: Chain B: A.212 Ligands: CLA.23 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:A.212 CLA.11: 5 residues within 4Å: Chain B: V.30 Ligands: CLA.12, CLA.15, CLA.19, CLA.22 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:V.30 CLA.12: 11 residues within 4Å: Chain B: L.12, R.18, A.22, H.23, H.26, V.237, L.238, S.241 Ligands: CLA.11, CLA.19, CLA.23 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:L.12, B:A.22, B:H.26 CLA.13: 4 residues within 4Å: Chain B: M.60, X.308, S.408, W.412 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:M.60, B:W.412, B:W.412, B:W.412, B:W.412 CLA.14: 6 residues within 4Å: Chain B: R.68, L.69, G.152, A.155 Ligands: CLA.16, CLA.17 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:R.68, B:L.69 CLA.15: 3 residues within 4Å: Chain B: A.248, A.249 Ligands: CLA.11 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:A.248 CLA.16: 6 residues within 4Å: Chain B: A.146, L.149, C.150, Y.193, H.201 Ligands: CLA.14 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:C.150 CLA.17: 6 residues within 4Å: Chain B: V.30, A.31, F.61, P.64, F.65 Ligands: CLA.14 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:P.64, B:F.65, B:F.65 CLA.18: 1 residues within 4Å: Chain B: A.243 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:A.243 CLA.19: 5 residues within 4Å: Chain B: H.9, A.22, W.115 Ligands: CLA.11, CLA.12 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:A.22, B:W.115 pi-Stacking: B:H.9 Metal complexes: B:H.9 CLA.20: 3 residues within 4Å: Chain B: V.198, A.200, A.204 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:A.200, B:A.204, B:A.204 CLA.21: 7 residues within 4Å: Chain B: L.19, I.20, H.23, M.138, I.141, H.142, L.145 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:I.20, B:H.23, B:M.138, B:I.141, B:L.145 CLA.22: 8 residues within 4Å: Chain B: H.9, T.10, L.423, F.426, G.427, H.428, W.430 Ligands: CLA.11 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:T.10, B:W.430 CLA.23: 6 residues within 4Å: Chain B: P.136, F.139, S.240, A.244 Ligands: CLA.10, CLA.12 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:F.139, B:S.240, B:A.244 CLA.24: 2 residues within 4Å: Chain B: L.24, A.110 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:L.24, B:A.110 CLA.25: 0 residues within 4Å: (No contacts) 0 PLIP interactions: CLA.26: 5 residues within 4Å: Chain C: C.244, G.247, G.248, W.266 Ligands: CLA.37 1 PLIP interactions: 1 interactions with chain C, Hydrophobic interactions: C:W.266 CLA.27: 7 residues within 4Å: Chain C: W.425, L.426, S.429, H.430 Chain J: D.14 Ligands: CLA.28, CLA.33 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:W.425, C:W.425, C:S.429, C:H.430 pi-Stacking: C:W.425 CLA.28: 9 residues within 4Å: Chain C: H.56, I.60 Chain J: P.17, P.20, V.21 Ligands: CLA.27, CLA.30, CLA.33, CLA.35 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain J, Hydrophobic interactions: C:I.60, J:V.21 pi-Stacking: C:H.56 pi-Cation interactions: C:H.56 CLA.29: 5 residues within 4Å: Chain A: S.124, G.128 Chain C: F.264, Y.274 Ligands: CLA.9 0 PLIP interactions: CLA.30: 9 residues within 4Å: Chain C: A.52, H.56, G.268, Y.271, L.272, S.275 Ligands: CLA.28, CLA.35, CLA.37 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:A.52, C:H.56, C:L.272 CLA.31: 4 residues within 4Å: Chain C: L.168, G.171, A.172, H.237 1 PLIP interactions: 1 interactions with chain C, Hydrophobic interactions: C:A.172 CLA.32: 1 residues within 4Å: Chain C: I.87 0 PLIP interactions: CLA.33: 7 residues within 4Å: Chain C: L.279, M.282, G.283, A.286, L.433 Ligands: CLA.27, CLA.28 0 PLIP interactions: CLA.34: 7 residues within 4Å: Chain C: L.49, L.50, H.53, F.163, H.164, V.167 Ligands: CLA.36 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:H.53, C:V.167 pi-Cation interactions: C:H.164 Metal complexes: C:H.164 CLA.35: 5 residues within 4Å: Chain C: F.436, F.437, G.440 Ligands: CLA.28, CLA.30 1 PLIP interactions: 1 interactions with chain C, Hydrophobic interactions: C:F.437 CLA.36: 6 residues within 4Å: Chain C: V.54, G.128, G.129, V.130, Y.131 Ligands: CLA.34 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:V.54, C:Y.131 CLA.37: 11 residues within 4Å: Chain C: G.162, H.164, W.266, Y.271, Y.274, S.275, L.276, A.278, L.279 Ligands: CLA.26, CLA.30 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:H.164, C:W.266, C:Y.271, C:Y.274, C:Y.274, C:S.275, C:A.278 CLA.39: 6 residues within 4Å: Chain D: F.184, F.188, G.200, V.201 Ligands: CLA.5, CLA.6 1 PLIP interactions: 1 interactions with chain D, Hydrophobic interactions: D:F.188 CLA.40: 8 residues within 4Å: Chain A: Q.199, V.202, A.203 Chain D: F.173, A.176, R.180 Ligands: CLA.5, PHO.7 1 PLIP interactions: 1 interactions with chain D, Hydrophobic interactions: D:F.173 CLA.42: 2 residues within 4Å: Chain D: F.113 Chain H: X.17 3 PLIP interactions: 3 interactions with chain D, Hydrophobic interactions: D:F.113, D:F.113, D:F.113 CLA.46: 0 residues within 4Å: (No contacts) 0 PLIP interactions: CLA.53: 10 residues within 4Å: Chain O: F.182, M.183, F.186, G.201, V.202, V.205, F.206 Ligands: CLA.85, CLA.86, CLA.87 3 PLIP interactions: 3 interactions with chain O, Hydrophobic interactions: O:F.186, O:V.205, O:F.206 CLA.55: 9 residues within 4Å: Chain O: I.36, P.39, T.40, H.92, Y.94, P.95, L.114, H.118, L.121 4 PLIP interactions: 4 interactions with chain O, Hydrophobic interactions: O:P.39, O:P.95, O:L.114, O:L.121 CLA.56: 1 residues within 4Å: Ligands: CLA.75 0 PLIP interactions: CLA.57: 2 residues within 4Å: Chain P: A.212 Ligands: CLA.70 1 PLIP interactions: 1 interactions with chain P, Hydrophobic interactions: P:A.212 CLA.58: 5 residues within 4Å: Chain P: V.30 Ligands: CLA.59, CLA.62, CLA.66, CLA.69 1 PLIP interactions: 1 interactions with chain P, Hydrophobic interactions: P:V.30 CLA.59: 11 residues within 4Å: Chain P: L.12, R.18, A.22, H.23, H.26, V.237, L.238, S.241 Ligands: CLA.58, CLA.66, CLA.69 3 PLIP interactions: 3 interactions with chain P, Hydrophobic interactions: P:L.12, P:A.22, P:H.26 CLA.60: 5 residues within 4Å: Chain P: M.60, X.308, S.408, W.412, F.413 3 PLIP interactions: 3 interactions with chain P, Hydrophobic interactions: P:M.60, P:W.412, P:W.412 CLA.61: 6 residues within 4Å: Chain P: R.68, L.69, G.152, A.155 Ligands: CLA.63, CLA.64 2 PLIP interactions: 2 interactions with chain P, Hydrophobic interactions: P:R.68, P:L.69 CLA.62: 3 residues within 4Å: Chain P: A.248, A.249 Ligands: CLA.58 1 PLIP interactions: 1 interactions with chain P, Hydrophobic interactions: P:A.248 CLA.63: 6 residues within 4Å: Chain P: A.146, L.149, C.150, Y.193, H.201 Ligands: CLA.61 1 PLIP interactions: 1 interactions with chain P, Hydrophobic interactions: P:C.150 CLA.64: 5 residues within 4Å: Chain P: A.31, F.61, P.64, F.65 Ligands: CLA.61 2 PLIP interactions: 2 interactions with chain P, Hydrophobic interactions: P:P.64, P:F.65 CLA.65: 2 residues within 4Å: Chain P: A.243 Ligands: CLA.70 1 PLIP interactions: 1 interactions with chain P, Hydrophobic interactions: P:A.243 CLA.66: 4 residues within 4Å: Chain P: A.22, W.115 Ligands: CLA.58, CLA.59 2 PLIP interactions: 2 interactions with chain P, Hydrophobic interactions: P:A.22, P:W.115 CLA.67: 4 residues within 4Å: Chain P: V.198, A.200, A.204, V.251 3 PLIP interactions: 3 interactions with chain P, Hydrophobic interactions: P:A.200, P:A.204, P:A.204 CLA.68: 7 residues within 4Å: Chain P: L.19, I.20, H.23, M.138, I.141, H.142, L.145 4 PLIP interactions: 4 interactions with chain P, Hydrophobic interactions: P:H.23, P:M.138, P:I.141, P:L.145 CLA.69: 6 residues within 4Å: Chain P: H.9, F.426, G.427, W.430 Ligands: CLA.58, CLA.59 5 PLIP interactions: 5 interactions with chain P, Hydrophobic interactions: P:F.426, P:W.430, P:W.430 pi-Stacking: P:W.430, P:W.430 CLA.70: 7 residues within 4Å: Chain P: P.136, F.139, H.142, S.240, A.244 Ligands: CLA.57, CLA.65 4 PLIP interactions: 4 interactions with chain P, Hydrophobic interactions: P:F.139, P:H.142, P:S.240, P:A.244 CLA.71: 3 residues within 4Å: Chain P: L.24, A.110, H.114 2 PLIP interactions: 2 interactions with chain P, Hydrophobic interactions: P:L.24, P:A.110 CLA.72: 0 residues within 4Å: (No contacts) 0 PLIP interactions: CLA.73: 5 residues within 4Å: Chain Q: C.244, G.247, G.248, T.255 Ligands: CLA.83 1 PLIP interactions: 1 interactions with chain Q, Hydrophobic interactions: Q:T.255 CLA.74: 7 residues within 4Å: Chain Q: W.425, L.426, S.429, H.430 Chain X: D.14 Ligands: CLA.79, CLA.93 5 PLIP interactions: 5 interactions with chain Q, Hydrophobic interactions: Q:W.425, Q:S.429, Q:H.430 pi-Stacking: Q:W.425, Q:W.425 CLA.75: 5 residues within 4Å: Chain O: S.124, G.128 Chain Q: Y.274, G.277 Ligands: CLA.56 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain Q, Hydrophobic interactions: O:S.124, Q:Y.274 CLA.76: 9 residues within 4Å: Chain Q: A.52, H.56, G.268, Y.271, L.272, S.275 Ligands: CLA.81, CLA.83, CLA.93 3 PLIP interactions: 3 interactions with chain Q, Hydrophobic interactions: Q:A.52, Q:H.56, Q:L.272 CLA.77: 3 residues within 4Å: Chain Q: L.168, A.172, H.237 1 PLIP interactions: 1 interactions with chain Q, Hydrophobic interactions: Q:A.172 CLA.78: 0 residues within 4Å: (No contacts) 0 PLIP interactions: CLA.79: 7 residues within 4Å: Chain Q: L.279, S.280, M.282, A.286, L.433 Ligands: CLA.74, CLA.93 1 PLIP interactions: 1 interactions with chain Q, Hydrophobic interactions: Q:A.286 CLA.80: 6 residues within 4Å: Chain Q: L.50, H.53, G.162, F.163, H.164, V.167 4 PLIP interactions: 4 interactions with chain Q, Hydrophobic interactions: Q:H.53, Q:V.167 pi-Cation interactions: Q:H.164 Metal complexes: Q:H.164 CLA.81: 5 residues within 4Å: Chain Q: F.436, F.437, G.440 Ligands: CLA.76, CLA.93 1 PLIP interactions: 1 interactions with chain Q, Hydrophobic interactions: Q:F.437 CLA.82: 5 residues within 4Å: Chain Q: L.125, G.128, G.129, V.130, Y.131 1 PLIP interactions: 1 interactions with chain Q, Hydrophobic interactions: Q:Y.131 CLA.83: 9 residues within 4Å: Chain Q: G.162, H.164, Y.271, Y.274, S.275, A.278, L.279 Ligands: CLA.73, CLA.76 7 PLIP interactions: 7 interactions with chain Q, Hydrophobic interactions: Q:H.164, Q:Y.271, Q:Y.271, Q:Y.274, Q:S.275, Q:A.278, Q:L.279 CLA.85: 5 residues within 4Å: Chain R: F.173, F.184, F.188, G.200 Ligands: CLA.53 3 PLIP interactions: 3 interactions with chain R, Hydrophobic interactions: R:F.173, R:F.184, R:F.188 CLA.86: 7 residues within 4Å: Chain O: F.158, G.178 Chain R: H.197, M.198, V.201 Ligands: CLA.53, PHO.88 1 PLIP interactions: 1 interactions with chain O, Hydrophobic interactions: O:F.158 CLA.87: 8 residues within 4Å: Chain O: Q.199, V.202, A.203 Chain R: F.173, A.176, R.180 Ligands: CLA.53, PHO.54 3 PLIP interactions: 2 interactions with chain R, 1 interactions with chain O, Hydrophobic interactions: R:F.173, R:R.180, O:A.203 CLA.89: 3 residues within 4Å: Chain R: P.39, W.104, H.117 2 PLIP interactions: 2 interactions with chain R, Hydrophobic interactions: R:P.39, R:W.104 CLA.92: 0 residues within 4Å: (No contacts) 0 PLIP interactions: CLA.93: 8 residues within 4Å: Chain Q: I.60 Chain X: P.17, P.20, V.21 Ligands: CLA.74, CLA.76, CLA.79, CLA.81 2 PLIP interactions: 1 interactions with chain X, 1 interactions with chain Q, Hydrophobic interactions: X:V.21, Q:I.60

4 x PHO: PHEOPHYTIN A(Non-covalent)(Covalent)

PHO.7: 6 residues within 4Å: Chain A: L.210 Chain D: I.144, A.145, A.148, G.278 Ligands: CLA.40 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.145, D:A.148, A:L.210 PHO.41: 8 residues within 4Å: Chain A: Y.147, V.280 Chain D: L.205, A.208, L.209, A.212, I.213 Ligands: CLA.6 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:Y.147, A:V.280, D:A.208, D:L.209, D:A.212, D:I.213 PHO.54: 7 residues within 4Å: Chain O: L.210, A.213, M.214 Chain R: I.144, A.148, G.278 Ligands: CLA.87 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain R Hydrophobic interactions: O:L.210, O:A.213, O:M.214, R:A.148 PHO.88: 7 residues within 4Å: Chain O: Y.147 Chain R: L.205, A.208, L.209, A.212, I.213 Ligands: CLA.86 6 PLIP interactions: 5 interactions with chain R, 1 interactions with chain O Hydrophobic interactions: R:L.205, R:A.208, R:L.209, R:A.212, R:I.213, O:Y.147

2 x FE: FE (III) ION(Non-covalent)

FE.38: 1 residues within 4Å: Chain D: H.214 No protein-ligand interaction detected (PLIP) FE.84: 1 residues within 4Å: Chain R: H.214 No protein-ligand interaction detected (PLIP)

2 x PLA: 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID(Non-covalent)

PLA.43: 5 residues within 4Å: Chain D: I.213, H.214, T.217, F.257, K.264 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:T.217 PLA.90: 5 residues within 4Å: Chain R: I.213, H.214, T.217, F.257, K.264 1 PLIP interactions: 1 interactions with chain R Hydrophobic interactions: R:T.217

2 x BCR: BETA-CAROTENE(Non-covalent)(Non-functional Binders)

BCR.44: 3 residues within 4Å: Chain C: F.436 Chain D: W.48 Ligands: BCR.47 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.436, D:W.48 BCR.47: 1 residues within 4Å: Ligands: BCR.44 No protein-ligand interaction detected (PLIP)

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

HEM.45: 1 residues within 4Å: Chain E: I.26 1 PLIP interactions: 1 interactions with chain E, Hydrophobic interactions: E:I.26 HEM.48: 5 residues within 4Å: Chain M: F.33, C.37, C.40, H.41, H.92 7 PLIP interactions: 7 interactions with chain M, Hydrophobic interactions: M:F.33, M:C.40 pi-Stacking: M:H.41, M:H.41, M:H.92 Metal complexes: M:H.41, M:H.92 HEM.91: 1 residues within 4Å: Chain S: I.26 1 PLIP interactions: 1 interactions with chain S, Hydrophobic interactions: S:I.26 HEM.94: 5 residues within 4Å: Chain 0: F.33, C.37, C.40, H.41, H.92 7 PLIP interactions: 7 interactions with chain 0, Hydrophobic interactions: 0:F.33, 0:C.40 pi-Stacking: 0:H.41, 0:H.41, 0:H.92 Metal complexes: 0:H.41, 0:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kamiya, N. et al., Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution. Proc.Natl.Acad.Sci.USA (2003)

Release Date

2003-01-14

Peptides

Photosystem II: Subunit PsbA: AO
Photosystem II: Subunit PsbB: BP
Photosystem II: Subunit PsbC: CQ
Photosystem II: Subunit PsbD: DR
Photosystem II: Subunit PsbE: ES
Photosystem II: Subunit PsbF: FT
Photosystem II: Subunit PsbG: GU
Photosystem II: Subunit PsbH: HV
Photosystem II: Subunit PsbI: IW
Photosystem II: Subunit PsbK: JX
Photosystem II: Subunit PsbO: KY
Photosystem II: Subunit PsbU: LZ
Photosystem II: Subunit PsbV: M0
Photosystem II: Subunit PsbX: N1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O
J

B
B

P
L

C
C

Q
M

D
D

R
N

E
E

S
P

F
F

T
Q

G
G

U
R

H
H

V
S

I
I

W
T

J
K

X
W

K
O

Y
Y

L
U

Z
Z

M
V

0
0

N
X

1
1

Membrane

We predict this structure to be a membrane protein.
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Photosystem II: Subunit PsbA

Photosystem II: Subunit PsbB

Photosystem II: Subunit PsbC

Photosystem II: Subunit PsbD

Photosystem II: Subunit PsbE

Photosystem II: Subunit PsbF

Photosystem II: Subunit PsbG

Photosystem II: Subunit PsbH

Photosystem II: Subunit PsbI

Photosystem II: Subunit PsbK

Photosystem II: Subunit PsbO

Photosystem II: Subunit PsbU

Photosystem II: Subunit PsbV

Photosystem II: Subunit PsbX

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